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Wu J, Yu S, Wang Y, Zhu J, Zhang Z. New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference. Front Oncol 2022; 12:1018279. [PMID: 36313673 PMCID: PMC9606464 DOI: 10.3389/fonc.2022.1018279] [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: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.
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Affiliation(s)
- Junchao Wu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sijie Yu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yalan Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,*Correspondence: Zhenhua Zhang,
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2
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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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3
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Tiwari A, Ahmed W, Oikarinen S, Sherchan SP, Heikinheimo A, Jiang G, Simpson SL, Greaves J, Bivins A. Application of digital PCR for public health-related water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155663. [PMID: 35523326 DOI: 10.1016/j.scitotenv.2022.155663] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 05/25/2023]
Abstract
Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, Queensland, Australia
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA; Department of Biology, Morgan State University, Baltimore, MD 21251, USA; BioEnvironmental Science Program, Department of Biology, Morgan State University, Baltimore, MD 21251, USA
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Finnish Food Authority, Seinäjoki, Finland
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | | | - Justin Greaves
- School of Environmental Sustainability, Loyola University Chicago, 6364 N. Sheridan Rd, Chicago, IL 60660, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, LA, USA.
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4
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Yuan H, Gao W, Yin J, Chen K, Mu Y, Jin Q, Jia C, Cong H, Yu J, Zhao J. Detection of EGFR gene with a droplet digital PCR chip integrating a double-layer glass reservoir. Anal Biochem 2022; 656:114877. [DOI: 10.1016/j.ab.2022.114877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/01/2022]
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5
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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: 34] [Impact Index Per Article: 17.0] [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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6
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Månsson CT, Vad-Nielsen J, Meldgaard P, Nielsen AL, Sorensen BS. EGFR transcription in non-small-cell lung cancer tumours can be revealed in ctDNA by cell-free chromatin immunoprecipitation (cfChIP). Mol Oncol 2021; 15:2868-2876. [PMID: 34453867 PMCID: PMC8564636 DOI: 10.1002/1878-0261.13093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
Determination of tumour‐specific transcription based on liquid biopsies possesses a large diagnostic and prognostic potential in non‐small cell lung cancer (NSCLC). Cell‐free DNA (cfDNA) packed in nucleosomes mirrors the histone modification profiles present in the cells of origin. H3 lysine 36 trimethylation (H3K36me3)‐modified nucleosomes are associated with active genes, and therefore, cell‐free chromatin immunoprecipitation (cfChIP) of H3K36me3‐associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates. We hypothesized that cfChIP can delineate transcriptional status of genes harbouring somatic cancer mutations and analysed the recurrently observed EGFR‐L858R mutation as an example. In representative NSCLC cell lines, the relationship between wild‐type (WT) and mutated EGFR transcriptional activity and mRNA expression levels was analysed using H3K36me3 ChIP and EGFR mRNA reverse transcription quantitative PCR (RT‐qPCR), respectively. The ChIP analysis showed that both WT and mutated EGFR are transcribed and that mRNA is similarly expressed per EGFR copy. Based on this observation, we proceeded with EGFR cfChIP using blood plasma from NSCLC patients harbouring the EGFR‐L858R mutation. EGFR‐WT fragments can originate from both nontumour cells with no or low EGFR transcription and tumour cells with active EGFR transcription, whereas EGFR‐L858R fragments must specifically originate from tumour cells. H3K36me3 cfChIP followed by droplet digital PCR (ddPCR) revealed significantly higher enrichment of EGFR‐L858R compared to EGFR‐WT fragments. This is in alignment with EGFR‐L858R being actively transcribed in the NSCLC tumour cells. This study is proof‐of‐principle that cfChIP can be used to identify tumour‐specific transcriptional activity of mutated alleles, which can expand the utility of liquid biopsy‐based cfDNA analyses to enhance tumour diagnostics and therapeutics.
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Jiang M, Liao P, Sun Y, Shao X, Chen Z, Fei P, Wang J, Huang Y. Rotational scan digital LAMP for accurate quantitation of nucleic acids. LAB ON A CHIP 2021; 21:2265-2271. [PMID: 33908545 DOI: 10.1039/d1lc00114k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Digital quantitation of nucleic acids is precise and sensitive because of its molecular-level resolution. However, only several quantitation formats are common, especially pertaining to how one obtains digital signals from multiple droplets. Here we present rotational scan digital loop-mediated amplification, termed RS-dLAMP. Droplets generated by centrifugation undergo isothermal loop-mediated amplification (LAMP), and self-tile by gravitation into a tubular space between two coaxial cylinders, which are then rotated and scanned to acquire droplet fluorescence signals. RS-dLAMP is quantitatively comparable to commercial digital PCR, yet has higher throughput. Moreover, by sealing the sample throughout analysis, RS-dLAMP eliminates contamination, facilitating point-of-care diagnosis and other applications.
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Affiliation(s)
- Mengcheng Jiang
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Peiyu Liao
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Yue Sun
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xinyang Shao
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zitian Chen
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbin Wang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, China
| | - Yanyi Huang
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China and College of Chemistry and Molecular Engineering, and, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China and Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
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8
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Obradovic J, Todosijevic J, Jurisic V. Application of the conventional and novel methods in testing EGFR variants for NSCLC patients in the last 10 years through different regions: a systematic review. Mol Biol Rep 2021; 48:3593-3604. [PMID: 33973139 DOI: 10.1007/s11033-021-06379-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022]
Abstract
Variants in the epidermal growth factor receptor (EGFR) gene are recognized as predictors of therapy response and are correlated with progression-free and overall survival in non-small cell lung cancer (NSCLC) patients. Molecularly guided therapy needs precise and cost-effective molecular tests. This review focused primarily on screening or target methods for the EGFR variants detection with diagnostic and prognostic potential in the clinical research published papers. Concerning the inclusion and exclusion criteria, the search interval comprised available articles published from 2010 until 2020 in three electronic databases, ISI Web of Science, Pub Med, and Scopus. The analysis of eligible studies started with 5647 and obtained the final 987 full-text articles analyzed as clinical research. The regions comprised were Africa, America, Australia, Asia, Euro-Asia, Europe, or a consortium of different countries. All of the tested methods were applied prevalently in Asia. In clinical research, the polymerase chain reaction (PCR), followed by sequencing methods have been involved mostly over the years. The identified high-through output approaches evolved to improve the survival and quality of the NSCLC patient's life becoming more sensitive, specific, and cost-effective.
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Affiliation(s)
- Jasmina Obradovic
- Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Jovana Todosijevic
- Faculty of Science, Institute of Biology and Ecology, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Jurisic
- Faculty of Medical Sciences, University of Kragujevac, 34000, Kragujevac, Serbia.
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9
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Siggillino A, Ulivi P, Pasini L, Reda MS, Chiadini E, Tofanetti FR, Baglivo S, Metro G, Crinó L, Delmonte A, Minotti V, Roila F, Ludovini V. Detection of EGFR Mutations in Plasma Cell-Free Tumor DNA of TKI-Treated Advanced-NSCLC Patients by Three Methodologies: Scorpion-ARMS, PNAClamp, and Digital PCR. Diagnostics (Basel) 2020; 10:diagnostics10121062. [PMID: 33297595 PMCID: PMC7762356 DOI: 10.3390/diagnostics10121062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Analysis of circulating cell-free tumor DNA (cftDNA) has emerged as a specific and sensitive blood-based approach to detect epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients. Still, there is some debate on what should be the preferential clinical method for plasma-derived cftDNA analysis. We tested 31 NSCLC patients treated with anti-EGFR tyrosine kinase inhibitors (TKIs), at baseline and serially during therapy, by comparing three methodologies in detecting EGFR mutations (L858R, exon 19 deletion, and T790M) from plasma: scorpions-amplification refractory mutation system (ARMS) methodology by using EGFR Plasma RGQ PCR Kit-QIAGEN, peptide nucleic acid (PNA) clamp and PANA RealTyper integration by using PNAClamp EGFR-PANAGENE, and digital real time PCR by using QuantStudio 3D Digital PCR System-Thermo Fisher Scientific. Specificity was 100% for all three mutations, independently from the platform used. The sensitivity for L858R (42.86%) and T790M (100%) did not change based on the method, while the sensitivity for Del 19 differed markedly (Scorpion-ARMS 45%, PNAClamp 75%, and Digital PCR 85%). The detection rate was also higher (94.23%) as measured by Digital PCR, and when we monitored the evolution of EGFR mutations over time, it evidenced the extreme inter-patient heterogeneity in terms of levels of circulating mutated copies. In our study, Digital PCR showed the best correlation with tissue biopsy and the highest sensitivity to attain the potential clinical utility of monitoring plasma levels of EGFR mutations.
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Affiliation(s)
- Annamaria Siggillino
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (P.U.); (E.C.)
| | - Luigi Pasini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (P.U.); (E.C.)
- Correspondence:
| | - Maria Sole Reda
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Elisa Chiadini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (P.U.); (E.C.)
| | - Francesca Romana Tofanetti
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Sara Baglivo
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Giulio Metro
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Lucio Crinó
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (L.C.); (A.D.)
| | - Angelo Delmonte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (L.C.); (A.D.)
| | - Vincenzo Minotti
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Fausto Roila
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Vienna Ludovini
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
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Yin J, Zou Z, Yin F, Liang H, Hu Z, Fang W, Lv S, Zhang T, Wang B, Mu Y. A Self-Priming Digital Polymerase Chain Reaction Chip for Multiplex Genetic Analysis. ACS NANO 2020; 14:10385-10393. [PMID: 32794742 DOI: 10.1021/acsnano.0c04177] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Digital PCR (polymerase chain reaction) is a powerful and attractive tool for the quantification of nucleic acids. However, the multiplex detection capabilities of this system are limited or require expensive instrumentation and reagents, all of which can hinder multiplex detection goals. Here, we propose strategies toward solving these issues regarding digital PCR. We designed and tested a self-priming digital PCR chip containing 6-plex detection capabilities using monochrome fluorescence, which has six detection areas and four-layer structures. This strategy achieved multiplex digital detection by the use of self-priming to preintroduce the specific reaction mix to a certain detection area. This avoids competition when multiple primer pairs coexist, allowing for multiplexing in a shorter time while using less reagents and low-cost instruments. This also prevents the digital PCR chip from experiencing long sample introduction time and evaporation. For further validation, this multiplex digital PCR chip was used to detect five types of EGFR (epidermal growth factor receptor) gene mutations in 15 blood samples from lung cancer patients. We conclude that this technique can precisely quantify EGFR mutations in high-performance diagnostics. This multiplex digital detection chip is a simple and inexpensive test intended for liquid biopsies. It can be applied and used in prenatal diagnostics, the monitoring of residual disease, rapid pathogen detection, and many other procedures.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Zheyu Zou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Fangfang Yin
- Weifang People's Hospital, Weifang 261000, China
| | - Hongxiao Liang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Zhenming Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Weibo Fang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130000, China
| | - Tao Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Ben Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
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11
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Li G, Zhai Y, Liu H, Wang Z, Huang R, Jiang H, Feng Y, Chang Y, Wu F, Zeng F, Jiang T, Zhang W. RPP30, a transcriptional regulator, is a potential pathogenic factor in glioblastoma. Aging (Albany NY) 2020; 12:16155-16171. [PMID: 32702667 PMCID: PMC7485703 DOI: 10.18632/aging.103596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022]
Abstract
Background: Old age has been demonstrated to be a risk factor for GBM, but the underlying biological mechanism is still unclear. We designed this study intending to determine a mechanistic explanation for the link between age and pathogenesis in GBM. Results: The expression of RPP30, an independent prognostic factor in GBM, was negatively correlated with age in both tumor and non-tumor brain samples. However, the post-transcriptional modifications carried out by RPP30 were different in primary GBM and non-tumor brain samples. RPP30 affected protein expression of cancer pathways by performing RNA modifications. Further, we found that RPP30 was related to drug metabolism pathways important in GBM. The decreased expression of RPP30 in older patients might be a pathogenic factor for GBM. Conclusion: This study revealed the role of RPP30 in gliomagenesis and provided the theoretical foundation for targeted therapy. Methods: In total, 616 primary GBM samples and 41 non-tumor brain samples were enrolled in this study. Transcriptome data and clinical information were obtained from the CGGA, TCGA, and GSE53890 databases. Gene Set Variation Analysis and Gene Ontology analyses were the primary analytical methods used in this study. All statistical analyses were performed using R.
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Affiliation(s)
- Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - You Zhai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Hanjie Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhiliang Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Ruoyu Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Haoyu Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuemei Feng
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yuanhao Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Fan Zeng
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)
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12
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Droplet digital PCR enabled by microfluidic impact printing for absolute gene quantification. Talanta 2020; 211:120680. [DOI: 10.1016/j.talanta.2019.120680] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 01/01/2023]
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13
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de Melo-Silva AJ, Lucena JP, Hueneburg T. The evolution of molecular diagnosis using digital polymerase chain reaction to detect cancer via cell-free DNA and circulating tumor cells. Cell Biol Int 2019; 44:735-743. [PMID: 31829466 DOI: 10.1002/cbin.11286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]
Abstract
Cancer is one of the most important causes of death worldwide. The onset of cancer may be initiated due to a variety of factors such as environment, genetics or even due to personal lifestyle choices. To counteract this tremendous increase, the demand for a new technology has risen. By this means, the use of digital polymerase chain reaction (dPCR) has been shown to be a promising methodology in the early detection of many types of cancers. Furthermore, several researchers confirmed that the use of tumor cell-free DNA (cfDNA) and circulating tumor cells (CTC) in peripheral blood is essential in revealing an early prognosis of such diseases. Besides this, it was established that dPCR might be used in a much more efficient, accurate, and reliable manner to amplify a variety of genetic material up to the identification of mutations in hematological diseases. Therefore, this article demonstrates the differences between conventional PCR and dPCR as a molecular technique to detect the early onset of cancer. Furthermore, CTC and cfDNA were officially approved by the Food and Drug Administration as new biological biomarkers in cancer development and monitoring.
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Affiliation(s)
- Alex José de Melo-Silva
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Jessica Paula Lucena
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Thomas Hueneburg
- University of Technology Sydney, Sydney, 2007, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne-Vic, 3010 Parkeville VIC, Australia
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14
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Nong L, Zhang Z, Xiong Y, Zheng Y, Li X, Li D, He Q, Li T. Comparison of next-generation sequencing and immunohistochemistry analysis for targeted therapy-related genomic status in lung cancer patients. J Thorac Dis 2019; 11:4992-5003. [PMID: 32030215 DOI: 10.21037/jtd.2019.12.25] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Some drugs that target molecular pathways are available for the targeted treatment of lung cancer. Multiple tests are needed to detect the status of the known molecular targets to determine whether the patients can respond to the drugs. An integrated platform for various gene alteration detection including both mutations and rearrangements is necessary for patients, especially those without enough tissue. Methods In our study, detections of EGFR mutations, ALK rearrangement, ROS1 rearrangement, and alterations of other nine important lung cancer-related genes were integrated into a single next-generation sequencing (NGS) platform. The NGS analysis was performed in 107 cases of non-small cell lung cancer (NSCLC). Meanwhile, hot spots such as EGFR L858R, EGFR E746-A750Del mutations and gene rearrangement of ALK and ROS1 were detected by immunohistochemical (IHC) staining. Results NGS could explore various gene mutations and gene rearrangements with a reduced experiment time and lower amounts of tumor tissues than multiple IHC staining experiments. NGS results were more informative and reliable than IHC staining for EGFR gene alterations, especially for the exon 19 region. NGS could also increase the positive rate of ALK rearrangement and decrease the false positive results of ROS1 rearrangements detected by IHC staining. Conclusions NGS is effective for confirmation the status of various important lung cancer-related gene alterations. Furthermore, NGS is necessary for the confirmation of the IHC results of ALK and ROS1 rearrangements.
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Affiliation(s)
- Lin Nong
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | | | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Yalin Zheng
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Xin Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Dong Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Qiye He
- Singlera Genomics Inc., Shanghai 201318, China
| | - Ting Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
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15
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Huang JK, Fan L, Wang TY, Wu PS. A new primer construction technique that effectively increases amplification of rare mutant templates in samples. BMC Biotechnol 2019; 19:62. [PMID: 31443709 PMCID: PMC6708177 DOI: 10.1186/s12896-019-0555-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023] Open
Abstract
Background In personalized medicine, companion diagnostic tests provide additional information to help select a treatment option likely to be optimal for a patient. Although such tests include several techniques for detecting low levels of mutant genes in wild-type backgrounds with fairly high sensitivity, most tests are not specific, and may exhibit high false positive rates. In this study, we describe a new primer structure, named ‘stuntmer’, to selectively suppress amplification of wild-type templates, and promote amplification of mutant templates. Results A single stuntmer for a defined region of DNA can detect several kinds of mutations, including point mutations, deletions, and insertions. Stuntmer PCRs are also highly sensitive, being able to amplify mutant sequences that may make up as little as 0.1% of the DNA sample. Conclusion In conclusion, our technique, stuntmer PCR, can provide a simple, low-cost, highly sensitive, highly accurate, and highly specific platform for developing companion diagnostic tests. Electronic supplementary material The online version of this article (10.1186/s12896-019-0555-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jr-Kai Huang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Ling Fan
- Department of Nuclear Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tao-Yeuan Wang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Pao-Shu Wu
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan. .,Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan.
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16
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Abstract
Cell-free circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) can be found in the bloodstream of individuals with cancer and are increasingly being explored as biomarkers in various aspects of cancer management. The application of next-generation sequencing (NGS) technologies to ctDNA and CTC analysis are providing new opportunities to characterize the cancer genome from a simple blood test and can facilitate the ease with which tumor-specific genomic changes can be followed over time. The serial analysis of ctDNA and CTCs has enormous potential to provide insights into intratumor heterogeneity and clonal evolution during disease progression, and may ultimately allow noninvasive molecular disease monitoring to guide therapeutic decisions and improve patient outcomes.
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Affiliation(s)
- Sarah-Jane Dawson
- Divisions of Cancer Medicine and Research, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; Centre for Cancer Research, University of Melbourne, Melbourne 3010, Australia
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17
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Risberg B, Tsui DWY, Biggs H, Ruiz-Valdepenas Martin de Almagro A, Dawson SJ, Hodgkin C, Jones L, Parkinson C, Piskorz A, Marass F, Chandrananda D, Moore E, Morris J, Plagnol V, Rosenfeld N, Caldas C, Brenton JD, Gale D. Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients. J Mol Diagn 2018; 20:883-892. [PMID: 30165204 PMCID: PMC6197164 DOI: 10.1016/j.jmoldx.2018.07.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 01/26/2023] Open
Abstract
Circulating tumor DNA (ctDNA) offers new opportunities for noninvasive cancer management. Detecting ctDNA in plasma is challenging because it constitutes only a minor fraction of the total cell-free DNA (cfDNA). Pre-analytical factors affect cfDNA levels contributed from leukocyte lysis, hence the ability to detect low-frequency mutant alleles. This study investigates the effects of the delay in processing, storage temperatures, different blood collection tubes, centrifugation protocols, and sample shipment on cfDNA levels. Peripheral blood (n = 231) from cancer patients (n = 62) were collected into K3EDTA or Cell-free DNA BCT tubes and analyzed by digital PCR, targeted amplicon, or shallow whole-genome sequencing. To assess pre-analytic effects, plasma was processed under different conditions after 0, 6, 24, 48, 96 hours, and 1 week at room temperature or 4°C, or using different centrifugation protocols. Digital PCR showed that cfDNA levels increased gradually with time in K3EDTA tubes, but were stable in BCT tubes. K3EDTA samples stored at 4°C showed less variation than room temperature storage, but levels were elevated compared with BCT. A second centrifugation at 3000 × g gave similar cfDNA yields compared with higher-speed centrifugation. Next-generation sequencing showed negligible differences in background error or copy number changes between K3EDTA and BCT, or following shipment in BCT. This study provides insights into the effects of sample processing on ctDNA analysis.
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Affiliation(s)
- Bente Risberg
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Dana W Y Tsui
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom.
| | - Heather Biggs
- Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Andrea Ruiz-Valdepenas Martin de Almagro
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Sarah-Jane Dawson
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Charlotte Hodgkin
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Linda Jones
- Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Christine Parkinson
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Elizabeth Moore
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom.
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18
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Gao W, Huang T, Yuan H, Yang J, Jin Q, Jia C, Mao G, Zhao J. Highly sensitive detection and mutational analysis of lung cancer circulating tumor cells using integrated combined immunomagnetic beads with a droplet digital PCR chip. Talanta 2018; 185:229-236. [DOI: 10.1016/j.talanta.2018.03.083] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/14/2018] [Accepted: 03/25/2018] [Indexed: 12/24/2022]
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19
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Tsui DWY, Murtaza M, Wong ASC, Rueda OM, Smith CG, Chandrananda D, Soo RA, Lim HL, Goh BC, Caldas C, Forshew T, Gale D, Liu W, Morris J, Marass F, Eisen T, Chin TM, Rosenfeld N. Dynamics of multiple resistance mechanisms in plasma DNA during EGFR-targeted therapies in non-small cell lung cancer. EMBO Mol Med 2018; 10:e7945. [PMID: 29848757 PMCID: PMC5991591 DOI: 10.15252/emmm.201707945] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 12/14/2022] Open
Abstract
Tumour heterogeneity leads to the development of multiple resistance mechanisms during targeted therapies. Identifying the dominant driver(s) is critical for treatment decision. We studied the relative dynamics of multiple oncogenic drivers in longitudinal plasma of 50 EGFR-mutant non-small-cell lung cancer patients receiving gefitinib and hydroxychloroquine. We performed digital PCR and targeted sequencing on samples from all patients and shallow whole-genome sequencing on samples from three patients who underwent histological transformation to small-cell lung cancer. In 43 patients with known EGFR mutations from tumour, we identified them accurately in plasma of 41 patients (95%, 41/43). We also found additional mutations, including EGFR T790M (31/50, 62%), TP53 (23/50, 46%), PIK3CA (7/50, 14%) and PTEN (4/50, 8%). Patients with both TP53 and EGFR mutations before treatment had worse overall survival than those with only EGFR Patients who progressed without T790M had worse PFS during TKI continuation and developed alternative alterations, including small-cell lung cancer-associated copy number changes and TP53 mutations, that tracked subsequent treatment responses. Longitudinal plasma analysis can help identify dominant resistance mechanisms, including non-druggable genetic information that may guide clinical management.
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Affiliation(s)
- Dana Wai Yi Tsui
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Muhammed Murtaza
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alvin Seng Cheong Wong
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Ross A Soo
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
- Cancer Science Institute, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | | | - Boon Cher Goh
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
- Cancer Science Institute, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Health Partners, Cambridge, UK
| | - Tim Forshew
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Wei Liu
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
| | - Tim Eisen
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Health Partners, Cambridge, UK
- Oncology Early Clinical Development, AstraZeneca, Cambridge, UK
| | - Tan Min Chin
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
- Cancer Science Institute, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
- Raffles Cancer Centre, Raffles Hospital, Singapore, Singapore
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Center - Cambridge, Cambridge, UK
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20
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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: 141] [Impact Index Per Article: 23.5] [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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21
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Li X, Zhou C. Comparison of cross-platform technologies for EGFR T790M testing in patients with non-small cell lung cancer. Oncotarget 2017; 8:100801-100818. [PMID: 29246024 PMCID: PMC5725066 DOI: 10.18632/oncotarget.19007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
Somatic mutations in the gene encoding epidermal growth factor receptor (EGFR) play an important role in determining targeted treatment modalities in non-small cell lung cancer (NSCLC). The EGFR T790M mutation emerges in approximately 50% of cases who acquire resistance to tyrosine kinase inhibitors. Detecting EGFR T790M mutation in tumor tissue is challenging due to heterogeneity of the tumor, low abundance of the mutation and difficulty for re-biopsy in patients with advanced disease. Alternatively, circulating tumor DNA (ctDNA) has been proposed as a non-invasive method for mutational analysis. The presence of EGFR mutations in ctDNA predicts response to the EGFR TKIs in the first-line setting. Molecular testing is now considered a standard care for NSCLC. The advent of standard commercially available kits and targeted mutational analysis has revolutionized the accuracy of mutation detection platforms for detection of EGFR mutations. Our review provides an overview of various commonly used platforms for detecting EGFR T790M mutation in tumor tissue and plasma.
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Affiliation(s)
- Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Pulmonary Cancer institute, Tongji University School of Medicine, Shanghai, P. R. China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Tongji University Medical School Cancer Institute, Shanghai, P. R. China
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22
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Shao Y, Zhong D. [Detection and Clinical Significance of Abundance of EGFR Mutation]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2017; 20:578-583. [PMID: 28855040 DOI: 10.3779/j.issn.1009-3419.2017.08.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Non-small cell lung cancer (NSCLC) patients, with sensitive epidermal growth factor receptor (EGFR) mutations react well to tyrosine kinase inhibitors (TKIs). However, the efficacy of TKIs on patients with the same mutant types differs dramatically. It is implied that the different quantities of mutant alleles could be one of the reasons underlying. Patients with high abundance of EGFR mutation might benefit more from TKIs. There are no universal standards for the definition of EGFR mutant abundance. Abundance could be semi-quantified according to the different sensitivities of detection methods, quantified with quantifying detection techniques such as digital PCR or next generation sequencing, or quantified based on the expression of mutant proteins. The different abundances of primary and metastatic diseases could reflect the heterogeneity of the tumors. The pre-treatment level or the dynamic change of EGFR mutant abundance could help observe the course of the diseases and predict the efficacy of TKIs. TKIs resistance could be detected by change of abundance prior to image manifestations. Besides, the abundance of T790M could also predict drug efficacy and resistance of the first and third generation TKIs. Thus the detection of EGFR mutant abundance has important clinical significance. The standardization and correction of abundance needs more exploration.
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Affiliation(s)
- Yi Shao
- Department of Medical Oncology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Diansheng Zhong
- Department of Medical Oncology, Tianjin Medical University General Hospital, Tianjin 300052, China
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23
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Liang Z, Cheng Y, Chen Y, Hu Y, Liu WP, Lu Y, Wang J, Wang Y, Wu G, Ying JM, Zhang HL, Zhang XC, Wu YL. EGFR T790M ctDNA testing platforms and their role as companion diagnostics: Correlation with clinical outcomes to EGFR-TKIs. Cancer Lett 2017. [PMID: 28642172 DOI: 10.1016/j.canlet.2017.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Somatic mutation in the epidermal growth factor receptor (EGFR) predict clinical response to EGFR tyrosine kinase inhibitors in non-small cell lung cancer (NSCLC) and is a promising target for personalised medicine. EGFR mutations have prognostic value. Initially patients respond well to tyrosine kinase inhibitors but finally they would develop resistance and about 50% of this resistance can be attributed to the emergence of EGFR resistant mutation, T790M. This necessitates the need for genetic testing for clinical management of patients. Molecular testing has become the standard of care in patients with NSCLCs based on the recommendations of standard guidelines. Though there are several platforms for EGFR mutation detection, highly sensitive platforms for clinical applicability as companion diagnostics for ctDNA based testing are emerging. Due to the dynamic changes in the T790M mutation during tyrosine kinase inhibitor (TKI) treatment, real-time monitoring of these genetic alterations is mandate for planning treatment strategies. With the advent of third generation TKIs that potentially target T790M, improvement in clinical outcome is documented in patients with NSCLCs. Managing these outcomes with appropriate companion diagnostics using ctDNA in early detection of these genetic alterations will improve patient care.
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Affiliation(s)
- Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Cheng
- Department of Oncology, Jilin Provincial Cancer Hospital, Changchun, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanping Hu
- Department of Oncology, Hubei Cancer Hospital, Wuhan, China
| | - Wei-Ping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - You Lu
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Centre, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ye Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Ming Ying
- Department of Pathology, National Cancer Centre, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He-Long Zhang
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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24
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Zhu Q, Xu Y, Qiu L, Ma C, Yu B, Song Q, Jin W, Jin Q, Liu J, Mu Y. A scalable self-priming fractal branching microchannel net chip for digital PCR. LAB ON A CHIP 2017; 17:1655-1665. [PMID: 28418438 DOI: 10.1039/c7lc00267j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR has been widely used in many bioresearch fields, such as next generation sequencing, single cell analysis, gene editing detection and so on. However, existing digital PCR methods still have some disadvantages, including high cost, sample loss, and complicated operation. In this work, we develop an exquisite scalable self-priming fractal branching microchannel net digital PCR chip. This chip with a special design inspired by natural fractal-tree systems has an even distribution and 100% compartmentalization of the sample without any sample loss, which is not available in existing chip-based digital PCR methods. A special 10 nm nano-waterproof layer was created to prevent the solution from evaporating. A vacuum pre-packaging method called self-priming reagent introduction is used to passively drive the reagent flow into the microchannel nets, so that this chip can realize sequential reagent loading and isolation within a couple of minutes, which is very suitable for point-of-care detection. When the number of positive microwells stays in the range of 100 to 4000, the relative uncertainty is below 5%, which means that one panel can detect an average of 101 to 15 374 molecules by the Poisson distribution. This chip is proved to have an excellent ability for single molecule detection and quantification of low expression of hHF-MSC stem cell markers. Due to its potential for high throughput, high density, low cost, lack of sample and reagent loss, self-priming even compartmentalization and simple operation, we envision that this device will significantly expand and extend the application range of digital PCR involving rare samples, liquid biopsy detection and point-of-care detection with higher sensitivity and accuracy.
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Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
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Determination of True ERBB2 Gene Amplification in Breast Cancer by Quantitative PCR Using a Reference and a Novel Control Gene. Appl Immunohistochem Mol Morphol 2016; 24:179-87. [PMID: 25789534 DOI: 10.1097/pai.0000000000000160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human epidermal growth factor receptor 2 (ERBB2/HER2) is amplified and overexpressed in 20% to 25% of breast carcinomas, correlates with poor outcome, and is an indication for treatment with trastuzumab. Accurate assessment of ERBB2 status is crucial for proper prognosis and to offer appropriate treatment for patients. ERBB2 status is generally determined by immunohistochemistry or fluorescence in situ hybridization (FISH), and sporadically by quantitative real-time polymerase chain reaction (PCR). We developed a new algorithm, termed quantitative PCR algorithm (QPA) score, and compared its performance with the gold standard FISH assay. The QPA is a computation of the relative number of copies of the ERBB2 gene with respect to a nonstandard, short-arm centromeric sequence on chromosome 17, and referenced to a single-copy gene, RPP30. This provides a more reliable determination of ERBB2 amplification, reducing the false polysomy 17 error. A total of 69 breast carcinoma samples were tested for quantitative real-time PCR and FISH, and the degree of concordance was analyzed. Sixty-two cases were in agreement between the 2 methods, and the contingency study assigned a κ value of 0.729 for their correlation. A receiver operating characteristic analysis was used to determine the optimal cut-off point for ERBB2 amplification, which was estimated at a QPA=1.53 (sensitivity=0.863; specificity=0.944). Our data conclude that the QPA is able to determine ERBB2 gene status with high accuracy, while also overcoming the limitations of conventional techniques and providing better cost-effectiveness.
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Beije N, Helmijr JC, Weerts MJ, Beaufort CM, Wiggin M, Marziali A, Verhoef C, Sleijfer S, Jansen MP, Martens JW. Somatic mutation detection using various targeted detection assays in paired samples of circulating tumor DNA, primary tumor and metastases from patients undergoing resection of colorectal liver metastases. Mol Oncol 2016; 10:1575-1584. [PMID: 28949453 PMCID: PMC5423131 DOI: 10.1016/j.molonc.2016.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/04/2016] [Accepted: 10/03/2016] [Indexed: 12/21/2022] Open
Abstract
Assessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in a minimally-invasive way. In a group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, from each patient DNA from cell-free DNA (cfDNA), the primary tumor, metastatic liver tissue, normal tumor-adjacent colon or liver tissue, and whole blood were obtained. Investigated was the feasibility of a targeted NGS approach to identify somatic mutations in ctDNA. This targeted NGS approach was also compared with NGS preceded by mutant allele enrichment using synchronous coefficient of drag alteration technology embodied in the OnTarget assay, and for selected mutations with digital PCR (dPCR). All tissue and cfDNA samples underwent IonPGM sequencing for a CRC-specific 21-gene panel, which was analyzed using a standard and a modified calling pipeline. In addition, cfDNA, whole blood and normal tissue DNA were analyzed with the OnTarget assay and with dPCR for specific mutations in cfDNA as detected in the corresponding primary and/or metastatic tumor tissue. NGS with modified calling was superior to standard calling and detected ctDNA in the cfDNA of 10 patients harboring mutations in APC, ATM, CREBBP, FBXW7, KRAS, KMT2D, PIK3CA and TP53. Using this approach, variant allele frequencies in plasma ranged predominantly from 1 to 10%, resulting in limited concordance between ctDNA and the primary tumor (39%) and the metastases (55%). Concordance between ctDNA and tissue markedly improved when ctDNA was evaluated for KRAS, PIK3CA and TP53 mutations by the OnTarget assay (80%) and digital PCR (93%). Additionally, using these techniques mutations were observed in tumor-adjacent tissue with normal morphology in the majority of patients, which were not observed in whole blood. In conclusion, in these mCRC patients with oligometastatic disease NGS on cfDNA was feasible, but had limited sensitivity to detect all somatic mutations present in tissue. Digital PCR and mutant allele enrichment before NGS appeared to be more sensitive to detect somatic mutations.
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Affiliation(s)
- Nick Beije
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jean C. Helmijr
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marjolein J.A. Weerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Corine M. Beaufort
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - Cornelis Verhoef
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maurice P.H.M. Jansen
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W.M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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Xu S, Duan Y, Lou L, Tang F, Shou J, Wang G. Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncol Lett 2016; 12:4238-4244. [PMID: 27895798 DOI: 10.3892/ol.2016.5184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/05/2016] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to explore the influence of T790M neighboring single nucleotide polymorphism (SNP) on the sensitivity of amplification refractory mutation system (ARMS)-based T790M mutation assay. Three ARMS-quantitative polymerase chain reaction (qPCR) systems (system 1 had a forward ARMS primer without rs1050171, system 2 included a forward ARMS primer with rs1050171 and system 3 contained the above two forward ARMS primers) were used to detect the T790M mutation in two series plasmid samples and genomic DNA (gDNA) of the cell line H1975. A total of 670 formalin-fixed paraffin-embedded (FFPE) tumor samples from non-small cell lung cancer patients were used to detect the epidermal growth factor receptor (EGFR) gene T790M mutation by direct sequencing and ARMS-qPCR. The ARMS-qPCR system 1 effectively detected samples with as low as 1% T790M mutant plasmid 1 (without rs1050171) and with 50% T790M mutant plasmid 2 (with rs1050171), while the ARMS-qPCR system 2 detected samples with 20 and 50% T790M mutant plasmid 1, in addition to samples with 1% T790M mutant plasmid 2. For the ARMS-qPCR system 3, samples with as low as 1% T790M mutant plasmids 1 or 2 were effectively detected. For gDNA analysis of the cell line H1975, the T790M mutation was effectively detected by the ARMS-qPCR systems 2 and 3 (~50% mutation rate), but was detected with a low mutation abundance by the ARMS-qPCR system 1 (~1% mutation rate). Of the 670 FFPE samples, 5 cases were identified to have the T790M mutation by sequencing and by the ARMS-qPCR system 1. One sample (named N067), which was considered as T790M-negative by sequencing, was demonstrated to have the T790M mutation using the ARMS-qPCR system 1. Sample N094, which was variant homozygous for rs1050171 and was indicated to be T790M-negative by sequencing and by the ARMS-qPCR system 1, was identified to have the T790M mutation with the ARMS-qPCR system 3. The A-variant allele frequency of rs1050171 was observed to be 28.2% in the 670 FFPE tumor samples, while the presence of rs148188503 (c. C2355T, p. T785T) was observed in sample N558, and a novel SNP with a base substitution (c. T2375C) at position 792 (p. L792P) in exon 20 of the EGFR gene was observed in sample N310. rs1050171 is a high-frequency SNP located near T790M, and the mutation statuses of rs1050171 appear to influence the sensitivity of the ARMS-based T790M detection system, thus generating a 14.3% false-negative rate (1/7). The present study proposes the risk that target neighboring SNPs (as far as 8 bp away in the present study) may exert on the sensitivity of ARMS-based detection methods.
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Affiliation(s)
- Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liping Lou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Fengjuan Tang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Juan Shou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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Iwama E, Takayama K, Harada T, Okamoto I, Ookubo F, Kishimoto J, Baba E, Oda Y, Nakanishi Y. Highly sensitive and quantitative evaluation of the EGFR T790M mutation by nanofluidic digital PCR. Oncotarget 2016; 6:20466-73. [PMID: 26015401 PMCID: PMC4653018 DOI: 10.18632/oncotarget.4058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/20/2015] [Indexed: 12/27/2022] Open
Abstract
The mutation of T790M in EGFR is a major mechanism of resistance to treatment with EGFR-TKIs. Only qualitative detection (presence or absence) of T790M has been described to date, however. Digital PCR (dPCR) analysis has recently been applied to the quantitative detection of target molecules in cancer with high sensitivity. In the present study, 25 tumor samples (13 obtained before and 12 after EGFR-TKI treatment) from 18 NSCLC patients with activating EGFR mutations were evaluated for T790M with dPCR. The ratio of the number of T790M alleles to that of activating mutation alleles (T/A) was determined. dPCR detected T790M in all 25 samples. Although T790M was present in all pre-TKI samples from 13 patients, 10 of these patients had a low T/A ratio and manifested substantial tumor shrinkage during treatment with EGFR-TKIs. In six of seven patients for whom both pre- and post-TKI samples were available, the T/A ratio increased markedly during EGFR-TKI treatment. Highly sensitive dPCR thus detected T790M in all NSCLC patients harboring activating EGFR mutations whether or not they had received EGFR-TKI treatment. Not only highly sensitive but also quantitative detection of T790M is important for evaluation of the contribution of T790M to EGFR-TKI resistance.
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Affiliation(s)
- Eiji Iwama
- Faculty of Medical Sciences, Department of Comprehensive Clinical Oncology, Kyushu University, Fukuoka, Japan.,Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Takayama
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Taishi Harada
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Isamu Okamoto
- Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan
| | - Fumihiko Ookubo
- Division of Diagnostic Pathology, Kyushu University Hospital, Fukuoka, Japan
| | - Junji Kishimoto
- Department of Research and Development of Next Generation Medicine, Kyushu University, Fukuoka, Japan
| | - Eishi Baba
- Faculty of Medical Sciences, Department of Comprehensive Clinical Oncology, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoichi Nakanishi
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan
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Vynck M, Trypsteen W, Thas O, Vandekerckhove L, De Spiegelaere W. The Future of Digital Polymerase Chain Reaction in Virology. Mol Diagn Ther 2016; 20:437-47. [DOI: 10.1007/s40291-016-0224-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Premasekharan G, Gilbert E, Okimoto RA, Hamirani A, Lindquist KJ, Ngo VT, Roy R, Hough J, Edwards M, Paz R, Foye A, Sood R, Copren KA, Gubens M, Small EJ, Bivona TG, Collisson EA, Friedlander TW, Paris PL. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer. Cancer Lett 2016; 380:144-52. [PMID: 27343980 DOI: 10.1016/j.canlet.2016.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Improvements in technologies to yield purer circulating tumor cells (CTCs) will enable a broader range of clinical applications. We have previously demonstrated the use of a commercially available cell-adhesion matrix (CAM) assay to capture invasive CTCs (iCTCs). To improve the purity of the isolated iCTCs, here we used fluorescence-activated cell sorting (FACS) in combination with the CAM assay (CAM + FACS). Our results showed an increase of median purity from the CAM assay to CAM + FACS for the spiked-in cell lines and patient samples analyzed from three different metastatic cancer types: castration resistant prostate cancer (mCRPC), non-small cell lung cancer (mNSCLC) and pancreatic ductal adenocarcinoma cancer (mPDAC). Copy number profiles for spiked-in mCRPC cell line and mCRPC patient iCTCs were similar to expected mCRPC profiles and a matched biopsy. A somatic epidermal growth factor receptor (EGFR) mutation specific to mNSCLC was observed in the iCTCs recovered from EGFR(+) mNSCLC cell lines and patient samples. Next-generation sequencing (NGS) of spiked-in pancreatic cancer cell line and mPDAC patient iCTCs showed mPDAC common mutations. CAM + FACS iCTC enrichment enables multiple downstream genomic characterizations across different tumor types.
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Affiliation(s)
- Gayatri Premasekharan
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Elizabeth Gilbert
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ross A Okimoto
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ashiya Hamirani
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Karla J Lindquist
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Vy T Ngo
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ritu Roy
- Computational Biology Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Jeffrey Hough
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Edwards
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Rosa Paz
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Adam Foye
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Riddhi Sood
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kirsten A Copren
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Gubens
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric J Small
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Trever G Bivona
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric A Collisson
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Terence W Friedlander
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Pamela L Paris
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
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31
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Qin Z, Ljubimov VA, Zhou C, Tong Y, Liang J. Cell-free circulating tumor DNA in cancer. CHINESE JOURNAL OF CANCER 2016; 35:36. [PMID: 27056366 PMCID: PMC4823888 DOI: 10.1186/s40880-016-0092-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 02/07/2023]
Abstract
Cancer is a common cause of death worldwide. Despite significant advances in cancer treatments, the morbidity and mortality are still enormous. Tumor heterogeneity, especially intratumoral heterogeneity, is a significant reason underlying difficulties in tumor treatment and failure of a number of current therapeutic modalities, even of molecularly targeted therapies. The development of a virtually noninvasive “liquid biopsy” from the blood has been attempted to characterize tumor heterogeneity. This review focuses on cell-free circulating tumor DNA (ctDNA) in the bloodstream as a versatile biomarker. ctDNA analysis is an evolving field with many new methods being developed and optimized to be able to successfully extract and analyze ctDNA, which has vast clinical applications. ctDNA has the potential to accurately genotype the tumor and identify personalized genetic and epigenetic alterations of the entire tumor. In addition, ctDNA has the potential to accurately monitor tumor burden and treatment response, while also being able to monitor minimal residual disease, reducing the need for harmful adjuvant chemotherapy and allowing more rapid detection of relapse. There are still many challenges that need to be overcome prior to this biomarker getting wide adoption in the clinical world, including optimization, standardization, and large multicenter trials.
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Affiliation(s)
- Zhen Qin
- Department of Medicine, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90048, USA.,School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, P. R. China
| | - Vladimir A Ljubimov
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Cuiqi Zhou
- Department of Medicine, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90048, USA
| | - Yunguang Tong
- Department of Medicine, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90048, USA. .,Department of Pathology, Xinxiang Medical University, Xinxiang, 453003, Henan, P. R. China.
| | - Jimin Liang
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, P. R. China.
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Abstract
Circulating tumour DNA (ctDNA) is that fraction of circulating DNA that is derived from a patient's cancer. For a number of years, patients with haematological malignancies have had their disease diagnosed or monitored using tests based on detecting specific cytological or molecular biomarkers in blood. It has long been appreciated that the more common epithelial malignancies also shed DNA into the blood and that this tumour-derived DNA generally contributes a minor percentage of the overall cell-free DNA burden in peripheral blood. The biotech revolution has transformed our ability to detect, quantify and interpret genetic events. This has led to a renewed interest in the potential of using a simple blood test to both diagnose cancer and longitudinally monitor the response to medical interventions in patients with solid organ malignancies.In this review we provide a summary of the literature to date and describe the main attributes of the current analytical approaches to ctDNA. We then focus on the potential clinical applications. There is increasing evidence to support the routine analysis of ctDNA in clinical decision-making for certain subgroups of patients with so-called hotspot mutations, particularly in lung and colorectal cancer. With continued refinement and technological progress, non-invasive molecular biomarkers including of ctDNA may be clinically useful at all stages of cancer management from diagnosis to disease progression.
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Affiliation(s)
- E. Karampini
- From the Department of Asthma, Allergy and Lung Biology, King’s College London, London SE1 9RT, UK and
| | - F. McCaughan
- From the Department of Asthma, Allergy and Lung Biology, King’s College London, London SE1 9RT, UK and
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
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Abstract
Digital PCR is a robust PCR technique that enables precise and accurate absolute quantitation of target molecules by diluting and partitioning of the samples into numerous compartments. Automated partitioning can be attained by creating "water-in-oil" emulsion (emulsion-based digital PCR) or using a chip with microchannels (microfluidics-based digital PCR). We discuss the advantages and a wide variety of clinical applications of this technique. We describe the droplet digital RT-PCR protocol published by Jennings et al. for identification and absolute quantitation of BCR-ABL1 transcripts.
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Lund HL, Hughesman CB, McNeil K, Clemens S, Hocken K, Pettersson R, Karsan A, Foster LJ, Haynes C. Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR. Anal Bioanal Chem 2015; 408:1079-94. [DOI: 10.1007/s00216-015-9204-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 01/25/2023]
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Zhang AK. Chromogenic Assay for Lung Cancer-Related EGFR Exon 19 Hotspot Deletion Mutations. Genet Test Mol Biomarkers 2015; 20:18-23. [PMID: 26544543 DOI: 10.1089/gtmb.2015.0197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) deletion mutations are associated with the development of nonsmall-cell lung cancer (NSCLC) and can serve as useful biomarkers. AIM In the present study, a novel assay for the detection of EGFR hotspot mutations was designed to be highly sensitive and practically false-positive-free to harness the potential of detecting such mutations as biomarkers early in the diagnosis of NSCLC. The new assay draws from the polymerase chain reaction (PCR) for amplification, blue-white screening for initial allele discrimination, and Sanger sequencing for mutation confirmation. RESULTS Mutant plasmids were mixed with wild-type DNA in ratios from 1:10 to 1:1000, followed by PCR amplification, blue-white screening, and sequencing. Mutants were successfully sequence confirmed for mixtures at ratios of 1:300 and 1:1000, highlighting the assay's high sensitivity and low risk of false-positives due to confirmation by Sanger sequencing. CONCLUSION With high sensitivity and low false positives, the present assay is appealing as an aid in the early diagnosis of NSCLC through liquid biopsy. The highly customizable nature of the assay provides the possibility of applications in the early diagnosis of other cancer-related genes through nonsense-transformable mutations.
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Affiliation(s)
- Andy K Zhang
- Department of Molecular Diagnostics, Genotheramics, Inc. , San Diego, California
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Li Y, Miao X, Ling L. Triplex DNA: A new platform for polymerase chain reaction-based biosensor. Sci Rep 2015; 5:13010. [PMID: 26268575 PMCID: PMC4534768 DOI: 10.1038/srep13010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/10/2015] [Indexed: 01/20/2023] Open
Abstract
Non - specific PCR amplification and DNA contamination usually accompany with PCR process, to overcome these problems, here we establish a sensor for thrombin by sequence - specific recognition of the PCR product with molecular beacon through triplex formation. Probe A and probe B were designed for the sensor, upon addition of thrombin, two probes hybridized to each other and the probe B was extended in the presence of Klenow Fragment polymerase and dNTPs. The PCR amplification occurred with further addition of Taq DNA Polymerase and two primers, the PCR product was recognized by molecular beacon through triplex formation. The fluorescence intensity increased with the logarithm of the concentration of thrombin over the range from 1.0 × 10−12 M to 1.0 × 10−7 M, with a detection limit of 261 fM. Moreover, the effect of DNA contamination and non - specific amplification could be ignored completely in the proposed strategy.
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Affiliation(s)
- Yubin Li
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Liansheng Ling
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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Zota VE, Magliocco AM. Molecular Technologies in the Clinical Diagnostic Laboratory. Cancer Control 2015; 22:142-51. [PMID: 26068758 DOI: 10.1177/107327481502200204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND New technologies for molecular analysis are increasing our ability to diagnose cancer. METHODS Several molecular analysis technologies are reviewed and their use in the clinical laboratory is discussed. RESULTS Select key technologies, including polymerase chain reaction and next-generation sequencing, are helping transform our ability to analyze cancer specimens. As these technological advances become more and more incorporated into routine diagnostic testing, our classification systems are likely to be impacted and our approach to treatment transformed. The routine use of such technology also brings challenges for analysis and reimbursement. CONCLUSION These advances in technology will change the way we diagnose, monitor, and treat patients with cancer.
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Affiliation(s)
- Victor E Zota
- Department of Anatomic Pathology, Moffitt Cancer Center, Tampa, FL 33612, USA.
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Digital PCR validates 8q dosage as prognostic tool in uveal melanoma. PLoS One 2015; 10:e0116371. [PMID: 25764247 PMCID: PMC4357379 DOI: 10.1371/journal.pone.0116371] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/08/2014] [Indexed: 12/02/2022] Open
Abstract
Background Uveal melanoma (UM) development and progression is correlated with specific molecular changes. Recurrent mutations in GNAQ and GNA11 initiate UM development while tumour progression is correlated with monosomy of chromosome 3 and gain of chromosome 8q. Hence, molecular analysis of UM is useful for diagnosis and prognosis. The aim of this study is to evaluate the use of digital PCR (dPCR) for molecular analysis of UM. Methods A series of 66 UM was analysed with dPCR for three hotspot mutations in GNAQ/GNA11 with mutation specific probes. The status of chromosomes 3 and 8 were analysed with genomic probes. The results of dPCR analysis were cross-validated with Sanger sequencing, SNP array analysis, and karyotyping. Results Using dPCR, we were able to reconstitute the molecular profile of 66 enucleated UM. With digital PCR, GNAQ/GNA11 mutations were detected in 60 of the 66 UM. Sanger sequencing revealed three rare variants, and, combined, these assays revealed GNAQ/GNA11 mutations in 95% of UM. Monosomy 3 was present in 43 and chromosome 8 aberrations in 52 of the 66 UM. Survival analysis showed that increasing 8q copy numbers were positively correlated with metastasis risk. Conclusion Molecular analysis with dPCR is fast and sensitive. Just like the recurrent genomic aberrations of chromosome 3 and 8, hotspot mutations in GNAQ and GNA11 are effectively detected in heterogeneous samples. Increased sensitivity contributes to the number of mutations and chromosomal aberrations detected. Moreover, quantification of copy number with dPCR validated 8q dosage as a sensitive prognostic tool in UM, of which implementation in disease prediction models will further improve prognostication.
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Sundberg SO, Wittwer CT, Zhou L, Palais R, Dwight Z, Gale BK. Quasi-digital PCR: Enrichment and quantification of rare DNA variants. Biomed Microdevices 2015; 16:639-44. [PMID: 24781884 DOI: 10.1007/s10544-014-9866-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rare variant enrichment and quantification was achieved by allele-specific, competitive blocker, digital PCR for aiming to provide a noninvasive method for detecting rare DNA variants from circulating cells. The allele-specific blocking chemistry improves sensitivity and lowers assay cost over previously described digital PCR methods while the instrumentation allowed for rapid thermal cycling for faster turnaround time. Because the digital counting of the amplified variants occurs in the presence of many wild-type templates in each well, the method is called "quasi-digital PCR". A spinning disk was used to separate samples into 1000 wells, followed by rapid-cycle, allele-specific amplification in the presence of a molecular beacon that serves as both a blocker and digital indicator. Monte Carlo simulations gave similar results to Poisson distribution statistics for mean number of template molecules and provided an upper and lower bound at a specified confidence level and accounted for input DNA concentration variation. A 111 bp genomic DNA fragment including the BRAF p.V600E mutation (c.T1799A) was amplified with quasi-digital PCR using cycle times of 23 s. Dilution series confirmed that wild-type amplification was suppressed and that the sensitivity for the mutant allele was <0.01 % (43 mutant alleles amongst 500,000 wild-type alleles). The Monte Carlo method presented here is publically available on the internet and can calculate target concentration given digital data or predict digital data given target concentration.
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Affiliation(s)
- Scott O Sundberg
- Department of Pathology, University of Utah, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA,
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40
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Zhang BO, Xu CW, Shao Y, Wang HT, Wu YF, Song YY, Li XB, Zhang Z, Wang WJ, Li LQ, Cai CL. Comparison of droplet digital PCR and conventional quantitative PCR for measuring EGFR gene mutation. Exp Ther Med 2015; 9:1383-1388. [PMID: 25780439 PMCID: PMC4353752 DOI: 10.3892/etm.2015.2221] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 02/02/2023] Open
Abstract
Early detection of epidermal growth factor receptor (EGFR) mutation, particularly EGFR T790M mutation, is of clinical significance. The aim of the present study was to compare the performances of amplification refractory mutation system-based quantitative polymerase chain reaction (ARMS-qPCR) and droplet digital polymerase chain reaction (ddPCR) approaches in the detection of EGFR mutation and explore the feasibility of using ddPCR in the detection of samples with low mutation rates. EGFR gene mutations in plasmid samples with different T790M mutation rates (0.1-5%) and 10 clinical samples were detected using the ARMS-qPCR and ddPCR approaches. The results demonstrated that the ARMS-qPCR method stably detected the plasmid samples (6,000 copies) with 5 and 1% mutation rates, while the ddPCR approach reliably detected those with 5% (398 copies), 1% (57 copies), 0.5% (24 copies) and 0.1% (average 6 copies) mutation rates. For the 10 clinical samples, the results for nine samples by the ARMS-qPCR and ddPCR methods were consistent; however, the sample N006, indicated to be EGFR wild-type by ARMS-qPCR, was revealed to have a clear EGFR T790M mutation with seven copies of mutant alleles in a background of 6,000 wild-type copies using ddPCR technology. This study demonstrates the feasibility of applying the ddPCR system to detect EGFR mutation and identified the advantage of ddPCR in the detection of samples with a low EGFR mutation abundance, particularly the secondary EGFR T790M resistance mutation, which enables early diagnosis before acquired resistance to tyrosine kinase inhibitors becomes clinically detectable.
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Affiliation(s)
- B O Zhang
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Chun-Wei Xu
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Yun Shao
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Huai-Tao Wang
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Yong-Fang Wu
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Ye-Ying Song
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Xiao-Bing Li
- Department of Pathology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Zhe Zhang
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Wen-Jing Wang
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Li-Qiong Li
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Cong-Li Cai
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, Hubei 430075, P.R. China
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Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms. Sci Rep 2015; 5:7616. [PMID: 25556930 PMCID: PMC5154595 DOI: 10.1038/srep07616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/03/2014] [Indexed: 12/12/2022] Open
Abstract
The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.
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42
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Rapid and label-free amplification and detection assay for genotyping of cancer biomarker. Biosens Bioelectron 2014; 68:107-114. [PMID: 25569872 DOI: 10.1016/j.bios.2014.12.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/02/2014] [Accepted: 12/17/2014] [Indexed: 02/06/2023]
Abstract
As understanding of the molecular pathways that drive malignancy in human cancer improves, personalized genotype-based therapy in combination with the predictive biomarker for the efficacy of targeted therapy is becoming more popular in cancer management. Sanger sequencing, that has been the gold standard for mutation analysis in cancer since the 1970s, suffers from low sensitivity, complexity, and time-consuming and labor-intensive procedure. Although several PCR based molecular testing methods are being emerged, there is no universal assay available for genotyping of cancer biomarkers. Here we present a rapid, simple and sensitive assay for the detection of epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancers (NSCLCs). The assay employs a novel double mis-matched primer (DMP) set to improve the detection ability of isothermal solid-phase amplification/detection (ISAD) based on silicon microring biosensor. We show that the EGFR-DMP can detect EGFR gene mutations within 20 min in a label-free and real-time manner. The EGFR-DMP was able to detect a mutation in a sample containing only 1% of the mutant cells in a mixture of wild-type cells. Furthermore, to validate the proposed assay for potential applications in clinical diagnostics, we examined paraffin-embedded tissue samples from 10 NSCLC patients for the presence of EGFR mutations by performing EGFR-DMP and direct sequencing. The EGFR-DMP assay was able to rapidly detect the mutation, with high sensitivity and specificity. The EGFR-DMP assay offers a robust and sensitive approach for the rapid identification of the EGFR mutation. The high sensitivity and specificity and rapidity of this approach may make it useful for predicting the clinical response to targeted EGFR TKIs as a companion diagnostic.
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Cui J, Yin Y, Ma Q, Wang G, Olman V, Zhang Y, Chou WC, Hong CS, Zhang C, Cao S, Mao X, Li Y, Qin S, Zhao S, Jiang J, Hastings P, Li F, Xu Y. Comprehensive characterization of the genomic alterations in human gastric cancer. Int J Cancer 2014; 137:86-95. [PMID: 25422082 DOI: 10.1002/ijc.29352] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/17/2014] [Indexed: 12/27/2022]
Abstract
Gastric cancer is one of the most prevalent and aggressive cancers worldwide, and its molecular mechanism remains largely elusive. Here we report the genomic landscape in primary gastric adenocarcinoma of human, based on the complete genome sequences of five pairs of cancer and matching normal samples. In total, 103,464 somatic point mutations, including 407 nonsynonymous ones, were identified and the most recurrent mutations were harbored by Mucins (MUC3A and MUC12) and transcription factors (ZNF717, ZNF595 and TP53). 679 genomic rearrangements were detected, which affect 355 protein-coding genes; and 76 genes show copy number changes. Through mapping the boundaries of the rearranged regions to the folded three-dimensional structure of human chromosomes, we determined that 79.6% of the chromosomal rearrangements happen among DNA fragments in close spatial proximity, especially when two endpoints stay in a similar replication phase. We demonstrated evidences that microhomology-mediated break-induced replication was utilized as a mechanism in inducing ∼40.9% of the identified genomic changes in gastric tumor. Our data analyses revealed potential integrations of Helicobacter pylori DNA into the gastric cancer genomes. Overall a large set of novel genomic variations were detected in these gastric cancer genomes, which may be essential to the study of the genetic basis and molecular mechanism of the gastric tumorigenesis.
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Affiliation(s)
- Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE; Department of Biochemistry and Molecular Biology, Computational Systems Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, GA
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44
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Wang Z, Chen R, Wang S, Zhong J, Wu M, Zhao J, Duan J, Zhuo M, An T, Wang Y, Bai H, Wang J. Quantification and dynamic monitoring of EGFR T790M in plasma cell-free DNA by digital PCR for prognosis of EGFR-TKI treatment in advanced NSCLC. PLoS One 2014; 9:e110780. [PMID: 25405807 PMCID: PMC4236040 DOI: 10.1371/journal.pone.0110780] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/19/2014] [Indexed: 11/18/2022] Open
Abstract
Background Among advanced non-small cell lung cancer (NSCLC) patients with an acquired resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI), about 50% carry the T790M mutation, but this frequency in EGFR-TKI-naïve patients and dynamic change during therapy remains unclear. This study investigated the quantification and dynamic change of T790M mutation in plasma cell-free DNA (cf-DNA) of advanced NSCLC patients to assess the clinical outcomes of EGFR-TKI therapy. Materials and Methods We retrospectively investigated 135 patients with advanced NSCLC who obtained progression-free survival (PFS) after EGFR-TKI for >6 months for their EGFR sensitive mutations and T790M mutation in matched pre- and post-TKI plasma samples, using denaturing high-performance liquid chromatography (DHPLC), amplification refractory mutation system (ARMS), and digital-PCR (D-PCR). Real-time PCR was performed to measure c-MET amplification. Results Detection limit of D-PCR in assessing the T790M mutation was approximately 0.03%. D-PCR identified higher frequency of T790M than ARMS in pre-TKI (31.3% vs. 5.5%) and post-TKI (43.0% vs. 25.2%) plasma samples. Patients with pre-TKI T790M showed inferior PFS (8.9 vs. 12.1 months, p = 0.007) and overall survival (OS, 19.3 vs. 31.9 months, p = 0.001) compared with those without T790M. In patients harboring EGFR sensitive mutation, high quantities of pre-TKI T790M predicted poorer PFS (p = 0.001) on EGFR-TKI than low ones. Moreover, patients who experienced increased quantity of T790M during EGFR-TKI treatment showed superior PFS and OS compared with those with decreased changes (p = 0.044 and p = 0.015, respectively). Conclusion Qualitative and quantitative T790M in plasma cf-DNA by D-PCR provided a non-invasive and sensitive assay to predict EGFR-TKI prognosis.
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Affiliation(s)
- Zhijie Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Rui Chen
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Shuhang Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Jia Zhong
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Meina Wu
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Jun Zhao
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Jianchun Duan
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Minglei Zhuo
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Tongtong An
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Yuyan Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
| | - Hua Bai
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
- * E-mail: (HB); (JW)
| | - Jie Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Cancer Hospital & Beijing Institute for Cancer Research, Beijing, China
- * E-mail: (HB); (JW)
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45
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Liam CK, Leow HR, How SH, Pang YK, Chua KT, Lim BK, Lai NL, Kuan YC, Pailoor J, Rajadurai P. Epidermal growth factor receptor mutations in non- small cell lung cancers in a multiethnic malaysian patient population. Asian Pac J Cancer Prev 2014; 15:321-6. [PMID: 24528049 DOI: 10.7314/apjcp.2014.15.1.321] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) in non- small cell lung cancer (NSCLC) are predictive of response to EGFR-targeted therapy in advanced stages of disease. This study aimed to determine the frequency of EGFR mutations in NSCLCs and to correlate their presence with clinical characteristics in multiethnic Malaysian patients. MATERIALS AND METHODS In this prospective study, EGFR mutations in exons 18, 19, 20 and 21 in formalin-fixed paraffin-embedded biopsy specimens of consecutive NSCLC patients were asessed by real-time polymerase chain reaction. RESULTS EGFR mutations were detected in NSCLCs from 55 (36.4%) of a total of 151 patients, being significantly more common in females (62.5%) than in males (17.2%) [odds ratio (OR), 8.00; 95% confidence interval (CI), 3.77-16.98; p<0.001] and in never smokers (62.5%) than in ever smokers (12.7%) (OR, 11.50; 95%CI, 5.08-26.03; p<0.001). Mutations were more common in adenocarcinoma (39.4%) compared to non-adenocarcinoma NSCLCs (15.8%) (p=0.072). The mutation rates in patients of different ethnicities were not significantly different (p=0.08). Never smoking status was the only clinical feature that independently predicted the presence of EGFR mutations (adjusted OR, 5.94; 95%CI, 1.94- 18.17; p=0.002). CONCLUSIONS In Malaysian patients with NSCLC, the EGFR mutation rate was similar to that in other Asian populations. EGFR mutations were significantly more common in female patients and in never smokers. Never smoking status was the only independent predictor for the presence of EGFR mutations.
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Affiliation(s)
- Chong-Kin Liam
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia E-mail :
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Ignatiadis M, Dawson SJ. Circulating tumor cells and circulating tumor DNA for precision medicine: dream or reality? Ann Oncol 2014; 25:2304-2313. [PMID: 25336116 DOI: 10.1093/annonc/mdu480] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing studies have provided further evidence to support the notion that cancer is a disease characterized by Darwinian evolution. Today, we often fail to capture this evolution and treatment decisions, even in the metastatic setting, are often based on analysis of primary tumor diagnosed years ago. Currently, this is considered a major reason for treatment failures in cancer care. Recent technological advances in the detection and characterization of circulating tumor cells and circulating tumor DNA might address this and allow for treatment tailoring based on real-time monitoring of tumor evolution. In this review, we summarize the most important recent findings in the field, focusing on challenges and opportunities in moving these tools forward in clinical practice.
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Affiliation(s)
- M Ignatiadis
- Department of Medical Oncology and Breast Cancer Translational Research Laboratory, J. C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
| | - S-J Dawson
- Division of Cancer Medicine; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
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Mojtahedi M, Fouquier d'Hérouël A, Huang S. Direct elicitation of template concentration from quantification cycle (Cq) distributions in digital PCR. Nucleic Acids Res 2014; 42:e126. [PMID: 25104023 PMCID: PMC4176345 DOI: 10.1093/nar/gku603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Digital PCR (dPCR) exploits limiting dilution of a template into an array of PCR reactions. From this array the number of reactions that contain at least one (as opposed to zero) initial template is determined, allowing inferring the original template concentration. Here we present a novel protocol to efficiently infer the concentration of a sample and its optimal dilution for dPCR from few targeted qPCR assays. By taking advantage of the real-time amplification feature of qPCR as opposed to relying on endpoint PCR assessment as in standard dPCR prior knowledge of template concentration is not necessary. This eliminates the need for serial dilutions in a separate titration and reduces the number of necessary reactions. We describe the theory underlying our approach and discuss experimental moments that contribute to uncertainty. We present data from a controlled experiment where the initial template concentration is known as proof of principle and apply our method on directly monitoring transcript level change during cell differentiation as well as gauging amplicon numbers in cDNA samples after pre-amplification.
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Affiliation(s)
- Mitra Mojtahedi
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Aymeric Fouquier d'Hérouël
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA Luxembourg Centre for Systems Biomedicine, L-4362 Esch-sur-Alzette, Luxembourg
| | - Sui Huang
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
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Kinz E, Leiherer A, Lang AH, Drexel H, Muendlein A. Accurate quantitation of JAK2 V617F allele burden by array-based digital PCR. Int J Lab Hematol 2014; 37:217-24. [DOI: 10.1111/ijlh.12269] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/12/2014] [Indexed: 02/02/2023]
Affiliation(s)
- E. Kinz
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Private University of the Principality of Liechtenstein; Triesen Liechtenstein
| | - A. Leiherer
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Private University of the Principality of Liechtenstein; Triesen Liechtenstein
| | - A. H. Lang
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Department of Medicine and Cardiology; Academic Teaching Hospital Feldkirch; Feldkirch Austria
| | - H. Drexel
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
- Private University of the Principality of Liechtenstein; Triesen Liechtenstein
- Department of Medicine and Cardiology; Academic Teaching Hospital Feldkirch; Feldkirch Austria
- Drexel College University of Medicine; Philadelphia PA USA
| | - A. Muendlein
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT); Feldkirch Austria
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49
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Snapback primer mediated clamping PCR for detection of EGFR and KRAS mutations in NSCLC patients by high resolution melting analysis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:407537. [PMID: 24883309 PMCID: PMC4026848 DOI: 10.1155/2014/407537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 03/21/2014] [Indexed: 11/17/2022]
Abstract
Assays for detecting somatic mutations are requested with higher sensitivity and more convenience. Here, we describe snapback primer mediated allele clamping enrichment polymerase chain reaction (SPACE-PCR), a novel form of PCR that amplifies minority alleles selectively from mixtures. We replaced regular PCR with SPACE-PCR before sequencing or genotyping assays to improve mutation detection sensitivity by up to 100-fold in detecting EGFR and KRAS somatic mutations. Combined SPACE-PCR with analysis of snapback primer by high resolution melting (SPACE-HRM), the high sensitive system that enables a closed-tube detection of mutations after isolating mutants has been established, as low as 1/105–1/1000 mutant samples can be diagnosed. And finally, in a double-blind experiment of 150 cases of non-small-cell lung cancer (NSCLC) patients, compared with direct DNA sequencing and ADX-EGFR/KRAS mutation detection kit, up to 25% of the PCR-direct sequencing negative cases turned out to be positive in SPACE-HRM mutation tests; the specificity is 100%. Results demonstrated that the SPACE-HRM system we set up is a high sensitive assay that can be used for EGFR and KRAS allele enrichment and reliable detection. We anticipate that the method will be employed in multiple applications in the clinic, including diagnosis, scanner recurrence monitoring, and treatment management.
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50
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Manoj P. Droplet digital PCR technology promises new applications and research areas. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:742-6. [PMID: 24779593 DOI: 10.3109/19401736.2014.913168] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Digital Polymerase Chain Reaction (dPCR) is used to quantify nucleic acids and its applications are in the detection and precise quantification of low-level pathogens, rare genetic sequences, quantification of copy number variants, rare mutations and in relative gene expressions. Here the PCR is performed in large number of reaction chambers or partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid. Results are calculated by counting amplified target sequence (positive droplets) and the number of partitions in which there is no amplification (negative droplets). The mean number of target sequences was calculated by Poisson Algorithm. Poisson correction compensates the presence of more than one copy of target gene in any droplets. The method provides information with accuracy and precision which is highly reproducible and less susceptible to inhibitors than qPCR. It has been demonstrated in studying variations in gene sequences, such as copy number variants and point mutations, distinguishing differences between expression of nearly identical alleles, assessment of clinically relevant genetic variations and it is routinely used for clonal amplification of samples for NGS methods. dPCR enables more reliable predictors of tumor status and patient prognosis by absolute quantitation using reference normalizations. Rare mitochondrial DNA deletions associated with a range of diseases and disorders as well as aging can be accurately detected with droplet digital PCR.
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Affiliation(s)
- P Manoj
- a Rajiv Gandhi Centre for Biotechnology , Thycaud P.O. , Thiruvananthapuram , Kerala , India
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