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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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Wang K, Sang B, He L, Guo Y, Geng M, Zheng D, Xu X, Wu W. Construction of dPCR and qPCR integrated system based on commercially available low-cost hardware. Analyst 2022; 147:3494-3503. [PMID: 35772342 DOI: 10.1039/d2an00694d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent quantitative PCR (qPCR) and digital PCR (dPCR) are two mainstream nucleic acid quantification technologies. However, commercial dPCR and qPCR instruments have a low integration, a high price, and a large footprint. To solve these shortcomings, we introduce a compound PCR system with both qPCR and dPCR functions. All the hardware used in this compound PCR system is commercially available and low-cost, and free software was used to realize the absolute quantification of nucleic acids. The compound PCR provides two working modes. In the qPCR mode, thermal cycling is realized by controlling the reciprocating motion of the x axis. The heating rate is 1.25 °C s-1 and the cooling rate is 1.75 °C s-1. We performed amplification experiments of the PGEM-3zf (+)1 gene. The performance level was similar to commercial qPCR instruments. In the dPCR mode, the heating rate is 0.5 °C s-1 and the cooling rate is 0.6 °C s-1. We performed the UPE-Q gene amplification and used the sequential actions of the two-dimensional mechanical sliders to scan the reaction products and used the method of regional statistics and back-inference threshold to get test results. The result we got was 1208 copies per μL-1, which was similar to expectations.
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Affiliation(s)
- Kangning Wang
- Institute of biological and medical engineering, Guangdong Academy of Sciences, China.
| | - Benliang Sang
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Limin He
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, China
| | - Mingkun Geng
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dezhou Zheng
- College of Applied Physics and Materials, Wuyi University, China
| | - Xiaolong Xu
- School of Biotechnology and Health Sciences, Wuyi University, China
| | - Wenming Wu
- Institute of biological and medical engineering, Guangdong Academy of Sciences, China.
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Carvalho TM, Dourado RM, Nakatani SM, Barros Duarte CA, Ioshii SO, Riediger IN, Tuon FF, Winter Boldt AB. Digital PCR detection of EGFR somatic mutations in non-small-cell lung cancer formalin fixed paraffin embedded samples. Mol Cell Probes 2021; 58:101745. [PMID: 34089806 DOI: 10.1016/j.mcp.2021.101745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/18/2021] [Accepted: 05/30/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Digital PCR (dPCR) is proposed to replace real time PCR and Sanger sequencing for detection and quantification of rare mutations, frequently unnoticed in the mass of tumoral cells. Screening of endothelial growth factor receptor (EGFR) mutations is mandatory before treatment with EGFR-targeted therapy with small-molecule tyrosine kinase inhibitors, which has been approved for the treatment of advanced non-small-cell lung cancer (NSCLC). OBJECTIVE In order to establish a cost-effective method for detection of mutations, we optimized dPCR identification of EGFR mutations in exons 18-21, and determined dPCR sensitivity, limits of detection (LoD) and quantification (LoQ). METHODS For clinical validation, we compared the performance of dPCR and castPCR in 57 NSCL formalin fixed paraffin embedded samples and 10 lung cancer-free formalin fixed paraffin embedded samples. RESULTS EGFR mutations DEL19, p.L858R, p.G719X, p.L861Q and p.T790 M were detected by dPCR in 27 samples versus 11 detected by castPCR (p = 0.014). LoD was determined as 100 molecules of DNA/uL and LoQ as 1%. Most of the samples (87%) identified by competitive Allele-Specific TaqMan (castPCR) as wild-type and by dPCR as mutated, presented less than 10% mutated DNA molecules (mean 4.57%). Accuracy of dPCR was 94.44%, as measured with the assay recommended by the College of American Pathologists. CONCLUSION These results indicated higher sensibility and specificity of dPCR for screening EGFR mutations in NSCLC biopsies, compared to castPCR.
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Affiliation(s)
| | - Renata Montoro Dourado
- Laboratório de Genética Molecular Humana, Universidade Federal Do Paraná, Curitiba, Brazil; Laboratório Genoprimer, Diagnóstico Molecular e Medicina Personalizada, Curitiba, Brazil
| | - Sueli Massumi Nakatani
- Laboratório Genoprimer, Diagnóstico Molecular e Medicina Personalizada, Curitiba, Brazil
| | | | | | | | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, Pontificia Universidade Católica Do Paraná, Curitiba, Brazil
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AKT1 Mutations in Peripheral Bronchiolar Papilloma: Glandular Papilloma and Mixed Squamous Cell and Glandular Papilloma Is Distinct From Bronchiolar Adenoma. Am J Surg Pathol 2021; 45:119-126. [PMID: 32868527 DOI: 10.1097/pas.0000000000001573] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Glandular papilloma (GP) and mixed squamous cell and glandular papilloma (MP) are rare benign pulmonary tumors occurring in the bronchi. Bronchiolar adenoma (BA) was recently characterized as a pulmonary tumor exhibiting alveolar spread. Both GP/MP and BA are composed of a mixture of glandular, ciliated, squamous, and basal cells. We aimed to clarify whether GP/MP and BA represent the same tumor. We evaluated the detailed histologic characteristics of 11 cases involving pulmonary peripheral tumors that exhibited histologic features of GP/MP or BA, and performed genetic analyses using targeted panel sequencing, allele-specific polymerase chain reaction, and digital polymerase chain reaction. Histologically, 4 and 7 tumors were classified as GP/MP and BA, respectively. GP/MP showed endobronchiolar papillary growth with a pseudostratified or stratified epithelium. In contrast, 5 BAs showed a predominant flat structure with a bilayered or pseudostratified epithelium, whereas 2 BAs showed a GP/MP-like papillary architecture. The mean epithelial thickness in each tumor was significantly larger in GP/MPs and BAs with a GP/MP-like morphology (103 to 242 μm) than in flat-predominant BA (23 to 47 μm, P=0.0010). AKT1 E17K mutations were detected in all GP/MPs and BAs with GP/MP-like morphology but were absent in the 5 flat-predominant BAs. AKT1 mutations were always concurrent with BRAF or HRAS mutations, and the variant allele frequency or percentage of mutant copies of AKT1 mutations was equal to those of BRAF or HRAS mutations. GP/MPs are characterized by AKT1 mutations concurrent with BRAF or HRAS mutations. Peribronchiolar papillary tumors with AKT1 mutations may also be classified as GP/MP.
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Moreno-Manuel A, Calabuig-Fariñas S, Obrador-Hevia A, Blasco A, Fernández-Díaz A, Sirera R, Camps C, Jantus-Lewintre E. dPCR application in liquid biopsies: divide and conquer. Expert Rev Mol Diagn 2020; 21:3-15. [PMID: 33305634 DOI: 10.1080/14737159.2021.1860759] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Precision medicine is already a reality in oncology, since biomarker-driven therapies have clearly improved patient survival. Furthermore, a new, minimally invasive strategy termed 'liquid biopsy' (LB) has revolutionized the field by allowing comprehensive cancer genomic profiling through the analysis of circulating tumor DNA (ctDNA). However, its detection requires extremely sensitive and efficient technologies. A powerful molecular tool based on the principle of 'divide and conquer' has emerged to solve this problem. Thus, digital PCR (dPCR) allows absolute and accurate quantification of target molecules.Areas covered: In this review we will discuss the fundamentals of dPCR and the most common approaches used for partition of samples and quantification. The advantages and limitations of dPCR will be mentioned in the context of LB in oncology.Expert opinion: In our opinion, dPCR has proven to be one of the most sensitive methods available for LB analysis, albeit some aspects such as its capacity of multiplexing and protocol standardization still require further improvements. Furthermore, the increasing sensitivities and lower costs of next generation sequencing (NGS) methods position dPCR as a confirmatory and complementary technique for NGS results which will likely prove to be very useful for treatment monitoring and assessing minimal residual disease.
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Affiliation(s)
- Andrea Moreno-Manuel
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain
| | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,Department of Pathology, Universitat de València, València, Spain.,CIBERONC, Madrid, Spain
| | - Antonia Obrador-Hevia
- Group of Advanced Therapies and Biomarkers in Clinical Oncology, Health Research Institute of the Balearic Islands (Idisba), Son Espases University Hospital, Palma, Spain.,Molecular Diagnosis Unit, Son Espases University Hospital, Palma, Spain
| | - Ana Blasco
- CIBERONC, Madrid, Spain.,Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain
| | - Amaya Fernández-Díaz
- Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain
| | - Rafael Sirera
- Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,CIBERONC, Madrid, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,CIBERONC, Madrid, Spain.,Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain.,Department of Medicine, Universitat De València, Valencia, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,CIBERONC, Madrid, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
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Abstract
ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity. ctDNA has shown growing clinical interest for cancer diagnosis, prognosis, theragnostics, therapeutic monitoring, and clonal evolution tracking. A major technical limit for ctDNA analysis from body fluids is the extremely low proportion of ctDNA compared to non-malignant cell-free DNA, underscoring the need for highly sensitive and specific detection techniques. The control of pre-analytical procedures appears essential for optimal ctDNA analysis and need to be standardized for clinical research applications. This chapter provides insights into major current technologies for ctDNA detection. Overall, PCR-based techniques are able to detect limited molecular alterations and have a high sensitivity suitable for monitoring purposes while NGS-based approaches are broad range molecular screening assays more specifically indicated for treatment selection. We briefly reviewed new technical innovations that are now available for ctDNA detection.
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Affiliation(s)
- Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000, Nancy, France.
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