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Kim BH, Kwon M, Lee D, Park SW, Shin E. K-ras mutation detected by peptide nucleic acid-clamping polymerase chain reaction, Ki-67, S100P, and SMAD4 expression can improve the diagnostic accuracy of inconclusive pancreatic EUS-FNB specimens. Pancreatology 2024:S1424-3903(24)00104-2. [PMID: 38693041 DOI: 10.1016/j.pan.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVES We aimed to assess the diagnostic utility of an immunohistochemical panel including calcium-binding protein P, p53, Ki-67, and SMAD family member 4 and K-ras mutation for diagnosing pancreatic solid lesion specimens obtained by endoscopic ultrasound-guided fine-needle biopsy and to confirm their usefulness in histologically inconclusive cases. METHODS Immunohistochemistry and peptide nucleic acid-clamping polymerase chain reaction for K-ras mutation were performed on 96 endoscopic ultrasound-guided fine-needle biopsy specimens. The diagnostic efficacy of each marker and the combination of markers was calculated. The diagnostic performances of these markers were evaluated in 27 endoscopic ultrasound-guided fine-needle biopsy specimens with histologically inconclusive diagnoses. A classification tree was constructed. RESULTS K-ras mutation showed the highest accuracy and consistency. Positivity in more than two or three of the five markers showed high diagnostic accuracy (94.6 % and 93.6 %, respectively), and positivity for more than three markers showed the highest accuracy for inconclusive cases (92.0 %). A classification tree using K-ras mutation, Ki-67, S100P, and SMAD4 showed high diagnostic performance, with only two misclassifications in inconclusive cases. CONCLUSIONS K-ras mutation detection via peptide nucleic acid-clamping polymerase chain reaction is a stable and accurate method for distinguishing between pancreatic ductal adenocarcinoma and non-pancreatic ductal adenocarcinoma lesions. A classification tree using K-ras mutation, Ki-67, S100P, and SMAD4 helps increase the diagnostic accuracy of cases that are histologically difficult to diagnose.
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Affiliation(s)
- Bo-Hyung Kim
- Department of Clinical Pharmacology and Therapeutics, Kyung Hee University College of Medicine and Hospital, Seoul, South Korea.
| | - Minji Kwon
- Department of Statistics, Ewha Womans University, Seoul, South Korea.
| | - Donghwan Lee
- Department of Statistics, Ewha Womans University, Seoul, South Korea.
| | - Se Woo Park
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Gyeonggi-do, South Korea.
| | - Eun Shin
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Gyeonggi-do, South Korea.
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2
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Oliveira BB, Costa B, Morão B, Faias S, Veigas B, Pereira LP, Albuquerque C, Maio R, Cravo M, Fernandes AR, Baptista PV. Combining the amplification refractory mutation system and high-resolution melting analysis for KRAS mutation detection in clinical samples. Anal Bioanal Chem 2023; 415:2849-2863. [PMID: 37097304 PMCID: PMC10185647 DOI: 10.1007/s00216-023-04696-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
The success of personalized medicine depends on the discovery of biomarkers that allow oncologists to identify patients that will benefit from a particular targeted drug. Molecular tests are mostly performed using tumor samples, which may not be representative of the tumor's temporal and spatial heterogeneity. Liquid biopsies, and particularly the analysis of circulating tumor DNA, are emerging as an interesting means for diagnosis, prognosis, and predictive biomarker discovery. In this study, the amplification refractory mutation system (ARMS) coupled with high-resolution melting analysis (HRMA) was developed for detecting two of the most relevant KRAS mutations in codon 12. After optimization with commercial cancer cell lines, KRAS mutation screening was validated in tumor and plasma samples collected from patients with pancreatic ductal adenocarcinoma (PDAC), and the results were compared to those obtained by Sanger sequencing (SS) and droplet digital polymerase chain reaction (ddPCR). The developed ARMS-HRMA methodology stands out for its simplicity and reduced time to result when compared to both SS and ddPCR but showing high sensitivity and specificity for the detection of mutations in tumor and plasma samples. In fact, ARMS-HRMA scored 3 more mutations compared to SS (tumor samples T6, T7, and T12) and one more compared to ddPCR (tumor sample T7) in DNA extracted from tumors. For ctDNA from plasma samples, insufficient genetic material prevented the screening of all samples. Still, ARMS-HRMA allowed for scoring more mutations in comparison to SS and 1 more mutation in comparison to ddPCR (plasma sample P7). We propose that ARMS-HRMA might be used as a sensitive, specific, and simple method for the screening of low-level mutations in liquid biopsies, suitable for improving diagnosis and prognosis schemes.
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Affiliation(s)
- Beatriz B Oliveira
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Beatriz Costa
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | | | | | - Bruno Veigas
- AlmaScience, Campus de Caparica, 2829-519, Caparica, Portugal
| | - Lucília Pebre Pereira
- Unidade de Investigação Em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Rua Prof Lima Basto, 1099-023, Lisbon, Portugal
| | - Cristina Albuquerque
- Unidade de Investigação Em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Rua Prof Lima Basto, 1099-023, Lisbon, Portugal
| | - Rui Maio
- Hospital da Luz-Lisboa, Lisbon, Portugal
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Marília Cravo
- Hospital da Luz-Lisboa, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
| | - Pedro Viana Baptista
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
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3
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Lai Q, Chen W, Zhang Y, Liu Z. Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors. Analyst 2021; 146:5822-5835. [PMID: 34581324 DOI: 10.1039/d1an00765c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.
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Affiliation(s)
- Qingteng Lai
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Wei Chen
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China. .,Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Yanke Zhang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Zhengchun Liu
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
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4
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Fouz MF, Appella DH. PNA Clamping in Nucleic Acid Amplification Protocols to Detect Single Nucleotide Mutations Related to Cancer. Molecules 2020; 25:molecules25040786. [PMID: 32059456 PMCID: PMC7070360 DOI: 10.3390/molecules25040786] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 01/02/2023] Open
Abstract
This review describes the application of peptide nucleic acids (PNAs) as clamps that prevent nucleic acid amplification of wild-type DNA so that DNA with mutations may be observed. These methods are useful to detect single-nucleotide polymorphisms (SNPs) in cases where there is a small amount of mutated DNA relative to the amount of normal (unmutated/wild-type) DNA. Detecting SNPs arising from mutated DNA can be useful to diagnose various genetic diseases, and is especially important in cancer diagnostics for early detection, proper diagnosis, and monitoring of disease progression. Most examples use PNA clamps to inhibit PCR amplification of wild-type DNA to identify the presence of mutated DNA associated with various types of cancer.
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5
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Ouyang W, Han J. Universal amplification-free molecular diagnostics by billion-fold hierarchical nanofluidic concentration. Proc Natl Acad Sci U S A 2019; 116:16240-16249. [PMID: 31358642 PMCID: PMC6697892 DOI: 10.1073/pnas.1904513116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Rapid and reliable detection of ultralow-abundance nucleic acids and proteins in complex biological media may greatly advance clinical diagnostics and biotechnology development. Currently, nucleic acid tests rely on enzymatic processes for target amplification (e.g., PCR), which have many inherent issues restricting their implementation in diagnostics. On the other hand, there exist no protein amplification techniques, greatly limiting the development of protein-based diagnosis. We report a universal biomolecule enrichment technique termed hierarchical nanofluidic molecular enrichment system (HOLMES) for amplification-free molecular diagnostics using massively paralleled and hierarchically cascaded nanofluidic concentrators. HOLMES achieves billion-fold enrichment of both nucleic acids and proteins within 30 min, which not only overcomes many inherent issues of nucleic acid amplification but also provides unprecedented enrichment performance for protein analysis. HOLMES features the ability to selectively enrich target biomolecules and simultaneously deplete nontargets directly in complex crude samples, thereby enormously enhancing the signal-to-noise ratio of detection. We demonstrate the direct detection of attomolar nucleic acids in urine and serum within 35 min and HIV p24 protein in serum within 60 min. The performance of HOLMES is comparable to that of nucleic acid amplification tests and near million-fold improvement over standard enzyme-linked immunosorbent assay (ELISA) for protein detection, being much simpler and faster in both applications. We additionally measured human cardiac troponin I protein in 9 human plasma samples, and showed excellent agreement with ELISA and detection below the limit of ELISA. HOLMES is in an unparalleled position to unleash the potential of protein-based diagnosis.
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Affiliation(s)
- Wei Ouyang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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6
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Zhang Z, Qin W, Sun Y. Contribution of biomarkers for pancreatic cancer-associated new-onset diabetes to pancreatic cancer screening. Pathol Res Pract 2018; 214:1923-1928. [PMID: 30477640 DOI: 10.1016/j.prp.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/09/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Pancreatic cancer (PaC) is one of the deadliest types of tumor, and it is regarded as a fatal disease, with a 5-year survival rate less than 10%. Most clinical diagnoses for PaC are made at an advanced stage because of the insidious onset of the disease, which leads to an extremely poor prognosis. RECENT FINDINGS The relationship between diabetes mellitus (DM) and PaC has been established by several decades of research, and the prevalence of DM in patients with PaC has been reported to be 40%, with half of the patients having developed new-onset DM within 2 years or less. Increasing evidence suggests that new-onset DM is associated with a high prevalence of PaC, and PaC resection ameliorates DM. Therefore, screening for PaC may be needed in patients with newly developed DM. PURPOSE The objective of this review was to present our current understanding of biomarkers for PaC-associated new-onset DM (PCAND), to offer a perspective on the prospects and problems of using this strategy for early screening to differentiate PCAND from new-onset type 2 DM not associated with PaC and to suggest candidate biomarkers to use for PaC screening in patients with new-onset DM. Finding sensitive and specific biomarkers to manage these patients constitutes a challenge for the research community and for public health policies.
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Affiliation(s)
- Zhenjun Zhang
- Institute of Hepatobiliary and Pancreatic Diseases, School of Medicine, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, China
| | - Wenjie Qin
- Institute of Hepatobiliary and Pancreatic Diseases, School of Medicine, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, China
| | - Yuling Sun
- Institute of Hepatobiliary and Pancreatic Diseases, School of Medicine, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, China.
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7
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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8
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Chen I, Raymond VM, Geis JA, Collisson EA, Jensen BV, Hermann KL, Erlander MG, Tempero M, Johansen JS. Ultrasensitive plasma ctDNA KRAS assay for detection, prognosis, and assessment of therapeutic response in patients with unresectable pancreatic ductal adenocarcinoma. Oncotarget 2017; 8:97769-97786. [PMID: 29228650 PMCID: PMC5716690 DOI: 10.18632/oncotarget.22080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 10/11/2017] [Indexed: 12/18/2022] Open
Abstract
Precision oncology requires sensitive and specific clinical biomarkers. Carbohydrate Antigen 19-9 (CA19-9) is widely used in pancreatic ductal adenocarcinoma (PDA) but lacks sensitivity and specificity. Nearly all PDAs harbor somatic KRAS mutations, nominating circulating tumor DNA (ctDNA) KRAS as an alternative disease biomarker, however, variable clinical performance has limited its clinical utility. We applied an ultrasensitive, PCR mutation enrichment, next generation sequencing ctDNA KRAS assay in a large cohort of patients with unresectable PDA (N = 189) recruited to the BIOPAC study between 2008-2015. Baseline and longitudinal serum CA19-9 and plasma ctDNA KRAS were correlated with time to progression (TTP) and overall survival (OS). Baseline ctDNA KRAS detection rate was 93.7% (86.4% in patients with non-elevated CA19-9). ctDNA KRAS and CA19-9 were positively correlated yet independently associated with TTP and OS (ctDNA KRAS p = 0.0018 and 0.0014; CA19-9 p = 0.0294 and 0.0007, respectively). A generated model quantitating longitudinal ctDNA KRAS correctly assessed greater than 80% of patient responses. Quantitative detection of KRAS ctDNA is an informative prognostic biomarker, complementary to CA19-9 in patients with unresectable PDA. Longitudinal ctDNA KRAS may inform therapeutic decision making and provides a kinetically dynamic and quantitative metric of patient response.
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Affiliation(s)
- Inna Chen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Eric A Collisson
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Benny V Jensen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kirstine L Hermann
- Department of Radiology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Margaret Tempero
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Julia S Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Medicine, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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10
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Zhao X, Lin CW. Rapid label-free visual detection of KRAS mutations using peptide nucleic acid and unmodified gold nanoparticles. RSC Adv 2017. [DOI: 10.1039/c7ra09088a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Colorectal cancer (CRC) is among the most commonly diagnosed cancers worldwide.
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Affiliation(s)
- Xihong Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education
- Key Laboratory for Hubei Novel Reactor & Green Chemical Technology
- Research Center for Environmental Ecology and Engineering
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
| | - Chii-Wann Lin
- Institute of Biomedical Engineering
- National Taiwan University
- Taipei 10617
- Taiwan
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11
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Zhao X, Chang CC, Chuang TL, Lin CW. Detection of KRAS mutations of colorectal cancer with peptide-nucleic-acid-mediated real-time PCR clamping. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1228479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Xihong Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology , Wuhan, China
- Institute of Biomedical Engineering, National Taiwan University , Taipei, Taiwan
| | - Chia-Chen Chang
- Institute of Biomedical Engineering, National Taiwan University , Taipei, Taiwan
| | - Tsung-Liang Chuang
- Institute of Biomedical Engineering, National Taiwan University , Taipei, Taiwan
| | - Chii-Wann Lin
- Institute of Biomedical Engineering, National Taiwan University , Taipei, Taiwan
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12
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Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Die Analyse von zirkulierender Tumor-DNA, zusammen mit der Analyse von zirkulierenden Tumorzellen auch oft Liquid Biopsy genannt, ist ein sich rasch entwickelndes Feld in der medizinischen Forschung. Obwohl es von der Entdeckung der zellfreien DNA bis hin zur Erkenntnis, dass sie sich als Biomarker eignet, Jahrzehnte gedauert hat, wurde der klinische Nutzen der ctDNA hinsichtlich der Überwachung des Therapieansprechens, der Identifizierung von Resistenzmechanismen und neu aufkommenden Therapiezielen sowie der Detektion von minimaler Resterkrankung mittlerweile in unzähligen Studien bewiesen.
Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar. In den letzten Jahren haben erhebliche technologische Fortschritte dazu beigetragen, dass eine Routineanwendung der ctDNA-Analysen tatsächlich realisierbar wird, sofern eine Reihe von regulatorischen Hürden überwunden wird.
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13
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Li Y, Fu XH, Yuan JQ, Yang ZY, Mao C, Dong XM, Tang JL, Wang SY. Colorectal cancer: using blood samples and tumor tissue to detect K-ras mutations. Expert Rev Anticancer Ther 2016; 15:715-25. [PMID: 26035720 DOI: 10.1586/14737140.2015.1037836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We performed a meta-analysis to assess whether blood can be substituted for tumor tissue in K-ras mutation testing. PubMed, EMBASE, MEDLINE, and BIOSIS databases were searched. Twenty-three studies including 1261 patients were included. The pooled overall sensitivity, specificity, and concordance rate were 0.69 (95% CI: 0.59-0.78), 0.96 (95% CI: 0.93-0.97), and 0.86 (95% CI: 0.82-0.89), respectively. Subgroup analysis indicated that plasma (sensitivity: 0.74; mutation rate: 0.34) exhibited superior sensitivity compared with serum (sensitivity: 0.45; mutation rate: 0.24). We conclude that blood is a suitable substitute for tumor tissue in K-ras mutation testing. K-ras mutation positivity in blood can be used to identify patients who should not receive EGFR monoclonal antibody therapy, but the absence of blood positivity does not necessarily imply negativity.
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Affiliation(s)
- Yang Li
- Center of Injury Prevention and Control, Medical College of Jinan University, Guangzhou, China
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14
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Tu M, Chia D, Wei F, Wong D. Liquid biopsy for detection of actionable oncogenic mutations in human cancers and electric field induced release and measurement liquid biopsy (eLB). Analyst 2016; 141:393-402. [PMID: 26645892 PMCID: PMC4701580 DOI: 10.1039/c5an01863c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oncogenic activations by mutations in key cancer genes such as EGFR and KRAS are frequently associated with human cancers. Molecular targeting of specific oncogenic mutations in human cancer is a major therapeutic inroad for anti-cancer drug therapy. In addition, progressive developments of oncogene mutations lead to drug resistance. Therefore, the ability to detect and continuously monitor key actionable oncogenic mutations is important to guide the use of targeted molecular therapies to improve long-term clinical outcomes in cancer patients. Current oncogenic mutation detection is based on direct sampling of cancer tissue by surgical resection or biopsy. Oncogenic mutations were recently shown to be detectable in circulating bodily fluids of cancer patients. This field of investigation, termed liquid biopsy, permits a less invasive means of assessing the oncogenic mutation profile of a patient. This paper will review the analytical strategies used to assess oncogenic mutations from biofluid samples. Clinical applications will also be discussed.
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Affiliation(s)
- Michael Tu
- School of Dentistry, University of California, Los Angeles, CA, USA.
| | - David Chia
- Department of Pathology, UCLA David Geffen School of Medicine at UCLA, Los Angeles, California, USA.
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, CA, USA.
| | - David Wong
- School of Dentistry, University of California, Los Angeles, CA, USA.
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15
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Huang JF, Zeng DZ, Duan GJ, Shi Y, Deng GH, Xia H, Xu HQ, Zhao N, Fu WL, Huang Q. Single-Tubed Wild-Type Blocking Quantitative PCR Detection Assay for the Sensitive Detection of Codon 12 and 13 KRAS Mutations. PLoS One 2015; 10:e0145698. [PMID: 26701781 PMCID: PMC4689371 DOI: 10.1371/journal.pone.0145698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023] Open
Abstract
The high degree of intra-tumor heterogeneity has meant that it is important to develop sensitive and selective assays to detect low-abundance KRAS mutations in metastatic colorectal carcinoma (mCRC) patients. As a major potential source of tumor DNA in the aforementioned genotyping assays, it was necessary to conduct an analysis on both the quality and quantity of DNA extracted from formalin-fixed paraffin-embedded (FFPE). Therefore, four commercial FFPE DNA extraction kits were initially compared with respect to their ability to facilitate extraction of amplifiable DNA. The results showed that TrimGen kits showed the greatest performance in relation to the quality and quantity of extracted FFPE DNA solutions. Using DNA extracted by TrimGen kits as a template for tumor genotyping, a real-time wild-type blocking PCR (WTB-PCR) assay was subsequently developed to detect the aforementioned KRAS mutations in mCRC patients. The results showed that WTB-PCR facilitated the detection of mutated alleles at a ratio of 1:10,000 (i.e. 0.01%) wild-type alleles. When the assay was subsequently used to test 49 mCRC patients, the results showed that the mutation detection levels of the WTB-PCR assay (61.8%; 30/49) were significantly higher than that of traditional PCR (38.8%; 19/49). Following the use of the real-time WTB-PCR assay, the ΔCq method was used to quantitatively analyze the mutation levels associated with KRAS in each FFPE sample. The results showed that the mutant levels ranged from 53.74 to 0.12% in the patients analyzed. In conclusion, the current real-time WTB-PCR is a rapid, simple, and low-cost method that permits the detection of trace amounts of the mutated KRAS gene.
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Affiliation(s)
- Jun-Fu Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Dong-Zhu Zeng
- Department of General Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Guang-Jie Duan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Yan Shi
- Department of General Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Guo-Hong Deng
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Han Xia
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Han-Qing Xu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Na Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
- * E-mail: (QH); (W-LF)
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
- * E-mail: (QH); (W-LF)
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Saliou A, Bidard FC, Lantz O, Stern MH, Vincent-Salomon A, Proudhon C, Pierga JY. Circulating tumor DNA for triple-negative breast cancer diagnosis and treatment decisions. Expert Rev Mol Diagn 2015; 16:39-50. [DOI: 10.1586/14737159.2016.1121100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Aarthy R, Mani S, Velusami S, Sundarsingh S, Rajkumar T. Role of Circulating Cell-Free DNA in Cancers. Mol Diagn Ther 2015; 19:339-50. [PMID: 26400814 DOI: 10.1007/s40291-015-0167-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liquid biopsy is a term used to describe non-invasive tests, which provide information about disease conditions through analysis of circulating cell-free DNA and circulating tumor cells from peripheral blood samples. In patients with cancer, the concentration of cell-free DNA increases, and structural, sequence, and epigenetic changes to DNA can be observed through the disease process and during therapy. Furthermore, cell-free DNA released by the tumor contains the same variants as those in the tumor cells. Therefore, cell-free DNA allows non-invasive assessment of cancer in real time. This review summarizes the origin of cell-free DNA, recent advancements in the detection of cell-free DNA, a possible role in metastasis, and its importance as a non-invasive diagnostic assay for cancer.
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Affiliation(s)
- Raghu Aarthy
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
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Atsumi J, Hanami T, Enokida Y, Ogawa H, Delobel D, Mitani Y, Kimura Y, Soma T, Tagami M, Takase Y, Ichihara T, Takeyoshi I, Usui K, Hayashizaki Y, Shimizu K. Eprobe-mediated screening system for somatic mutations in the KRAS locus. Oncol Rep 2015; 33:2719-27. [PMID: 25823645 PMCID: PMC4431451 DOI: 10.3892/or.2015.3883] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/03/2015] [Indexed: 12/21/2022] Open
Abstract
Activating mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) loci are largely predictive of resistance to epidermal growth factor receptor (EGFR) therapy in colorectal cancer (CRC). A highly sensitive detection system for the KRAS gene mutations is urgently needed; however, conventional methods have issues with feasibility and cost performance. Here, we describe a novel detection system using a fluorescence ‘Eprobe’ capable of detecting low level KRAS gene mutations, via real-time PCR, with high sensitivity and simple usability. We designed our Eprobes to be complementary to wild-type (WT) KRAS or to the commonly mutated codons 12 and 13. The WT Eprobe binds strongly to the WT DNA template and suppresses amplification by blocking annealing of the primer during PCR. Eprobe-PCR with WT Eprobe shows high sensitivity (0.05–0.1% of plasmid DNA, 1% of genomic DNA) for the KRAS mutation by enrichment of the mutant type (MT) amplicon. Assay performance was compared to Sanger sequencing using 92 CRC samples. Discrepancies were analyzed by mutation genotyping via Eprobe-PCR with full match Eprobes for 7 prevalent mutations and the next generation sequencing (NGS). Significantly, the Eprobe system had a higher sensitivity for detecting KRAS mutations in CRC patient samples; these mutations could not be identified by Sanger sequencing. Thus, the Eprobe approach provides for highly sensitive and convenient mutation detection and should be useful for diagnostic applications.
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Affiliation(s)
- Jun Atsumi
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takeshi Hanami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasuaki Enokida
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hiroomi Ogawa
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Diane Delobel
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasumasa Mitani
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasumasa Kimura
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Takahiro Soma
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Michihira Tagami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yoshiaki Takase
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tatsuo Ichihara
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Izumi Takeyoshi
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kengo Usui
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Kimihiro Shimizu
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
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LaConti JJ, Laiakis EC, Mays AD, Peran I, Kim SE, Shay JW, Riegel AT, Fornace AJ, Wellstein A. Distinct serum metabolomics profiles associated with malignant progression in the KrasG12D mouse model of pancreatic ductal adenocarcinoma. BMC Genomics 2015; 16 Suppl 1:S1. [PMID: 25923219 PMCID: PMC4315147 DOI: 10.1186/1471-2164-16-s1-s1] [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] [Indexed: 02/06/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer deaths worldwide with less than a 6% 5-year survival rate. PDAC is associated with poor prognosis based on the late stage diagnosis of the disease. Current diagnostic tests lack the sensitivity and specificity to identify markers of early staging. Metabolomics has provided biomarkers for various diseases, stressors, and environmental exposures. In this study we utilized the p48-Cre/LSL-KrasG12D mouse model with age-matched wild type mice. This model shows malignant progression to PDAC analogous to the human disease stages via early and late pancreatic intra-epithelial neoplasia (PanIN) lesions. Results Serum was collected from mice with early PanIN lesions (at 3-5 months) and with late PanIN or invasive PDAC lesions (13-16 months), as determined by histopathology. Metabolomics analysis of the serum samples was conducted through UPLC-TOFMS (Ultra Performance Liquid Chromatography coupled to Time-of-flight Mass Spectrometry). Multivariate data analysis revealed distinct metabolic patterns in serum samples collected during malignant progression towards invasive PDAC. Animals with early or late stage lesions were distinguished from their respective controls with 82.1% and 81.5% accuracy, respectively. This also held up for randomly selected subgroups in the late stage lesion group that showed less variability between animals. One of the metabolites, citrate, was validated through tandem mass spectrometry and showed increased levels in serum with disease progression. Furthermore, serum metabolite signatures from animals with early stage lesions identified controls and animals with late stage lesions with 81.5% accuracy (p<0.01) and vice-versa with 73.2% accuracy (p<0.01). Conclusions We conclude that metabolomics analysis of serum samples can identify the presence of early and late stage pancreatic cancer.
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Gu J, Wang D, Huang Y, Lu Y, Peng C. Diagnostic value of combining CA 19-9 and K-ras gene mutation in pancreatic carcinoma: a meta-analysis. Int J Clin Exp Med 2014; 7:3225-3234. [PMID: 25419353 PMCID: PMC4238530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/15/2014] [Indexed: 06/04/2023]
Abstract
AIMS To assess diagnostic value of Carbohydrate Antigen 19-9 (CA 19-9), combined CA 19-9 and K-ras mutation in plasma DNA in diagnosing patients with pancreatic carcinoma. MATERIALS AND METHODS MEDLINE, EMBASE, the Cochrane Library, Sinomed, CNKI and other databases, from established to November, 2013, were searched for initial studies. All the studies published in English or Chinese relating to the diagnostic value of CA 19-9 and K-ras gene mutation for patients with pancreatic cancer were collected. Methodological quality was assessed. The statistic software called "Meta-disc" (version 1.4) was used for data analysis. RESULTS 10 studies were included in this meta-analysis. The pooled sensitivity estimate for CA 19-9 (78%) was significantly higher than K-ras mutation (65%). While, for the specificity estimate, K-ras mutation (93%) was significantly higher than CA 19-9 (77%). The pooled DOR estimate for K-ras mutation (21.82) was significantly higher than CA 19-9 (18.36). SROC curves for K-ras mutation showed better diagnostic accuracy than CA 19-9. For CA 19-9 measurement, its diagnostic value decreased in differentiating pancreatic cancer for patients with pancreatitis, especially chronic process. CONCLUSION CA 19-9 was a high sensitive and K-ras was a high specific method in diagnosing patients with pancreatic cancer. These two modalities probably act different roles during different conditions in diagnosing pancreatic carcinoma.
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Affiliation(s)
- Jiangning Gu
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, People’s Republic of China
| | - Di Wang
- Department of Prophylactic Medicine, Shanghai First People’s Hospital, Shanghai Jiao Tong UniversityShanghai, People’s Republic of China
| | - Ya Huang
- Department of Endocrine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, People’s Republic of China
| | - Yi Lu
- Department of Gastroenterology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, People’s Republic of China
| | - Chenghong Peng
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, People’s Republic of China
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Jia Y, Sanchez JA, Wangh LJ. Kinetic hairpin oligonucleotide blockers for selective amplification of rare mutations. Sci Rep 2014; 4:5921. [PMID: 25082368 PMCID: PMC4118197 DOI: 10.1038/srep05921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/15/2014] [Indexed: 01/13/2023] Open
Abstract
Detection of rare mutant alleles in an excess of wild type alleles is increasingly important in cancer diagnosis. Several methods for selective amplification of a mutant allele via the polymerase chain reaction (PCR) have been reported, but each of these methods has its own limitations. A common problem is that Taq DNA polymerase errors early during amplification generate false positive mutations which also accumulate exponentially. In this paper, we described a novel method using hairpin oligonucleotide blockers that can selectively inhibit the amplification of wild type DNA during LATE-PCR amplification. LATE-PCR generates double-stranded DNA exponentially followed by linear amplification of single-stranded DNA. The efficiency of the blocker is optimized by adjusting the LATE-PCR temperature cycling profile. We also demonstrate that it is possible to minimize false positive signals caused by Taq DNA polymerase errors by using a mismatched excess primer plus a modified PCR profile to preferentially enrich for mutant target sequences prior to the start of the exponential phase of LATE-PCR amplification. In combination these procedures permit amplification of specific KRAS mutations in the presence of more than 10,000 fold excess of wild type DNA without false positive signals.
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Affiliation(s)
- Yanwei Jia
- 1] Department of Biology, Brandeis University, Waltham, MA 02453, USA [2] State Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macau, China
| | | | - Lawrence J Wangh
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
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22
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Bidard FC, Weigelt B, Reis-Filho JS. Going with the flow: from circulating tumor cells to DNA. Sci Transl Med 2014; 5:207ps14. [PMID: 24132635 DOI: 10.1126/scitranslmed.3006305] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular analyses of circulating tumor DNA (ctDNA) in plasma from cancer patients have the potential to deliver minimally invasive diagnostic and disease-monitoring biomarkers. Drawing from experience gained through the translation of circulating tumor cell detection to clinical tests, we discuss ctDNA as a source of tumor material for biomarker development.
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Castellanos-Rizaldos E, Milbury CA, Guha M, Makrigiorgos GM. COLD-PCR enriches low-level variant DNA sequences and increases the sensitivity of genetic testing. Methods Mol Biol 2014; 1102:623-39. [PMID: 24259002 DOI: 10.1007/978-1-62703-727-3_33] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Detection of low-level mutations is important for cancer biomarker and therapy targets discovery, but reliable detection remains a technical challenge. The newly developed method of CO-amplification at Lower Denaturation temperature PCR (COLD-PCR) helps to circumvent this issue. This PCR-based technology preferentially enriches minor known or unknown variants present in samples with a high background of wild type DNA which often hampers the accurate identification of these minority alleles. This is a simple process that consists of lowering the temperature at the denaturation step during the PCR-cycling protocol (critical denaturation temperature, T c) and inducing DNA heteroduplexing during an intermediate step. COLD-PCR in its simplest forms does not need additional reagents or specific instrumentation and thus, can easily replace conventional PCR and at the same time improve the mutation detection sensitivity limit of downstream technologies. COLD-PCR can be applied in two basic formats: fast-COLD-PCR that can enrich T m-reducing mutations and full-COLD-PCR that can enrich all mutations, though it requires an intermediate cross-hybridization step that lengthens the thermocycling program. An improved version of full-COLD-PCR (improved and complete enrichment, ice-COLD-PCR) has also been described. Finally, most recently, we developed yet another form of COLD-PCR, temperature-tolerant-COLD-PCR, which gradually increases the denaturation temperature during the COLD-PCR reaction, enriching diverse targets using a single cycling program. This report describes practical considerations for application of fast-, full-, ice-, and temperature-tolerant-COLD-PCR for enrichment of mutations prior to downstream screening.
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Affiliation(s)
- Elena Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Sensitivity of alternative testing for pancreaticobiliary cancer: a 10-y review of the literature. J Surg Res 2014; 190:535-47. [PMID: 24969546 DOI: 10.1016/j.jss.2014.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Biliary strictures present a diagnostic challenge to differentiate benign disease from hepatopancreaticobiliary (HPB) malignancies. Endoscopic retrograde cholangiopancreatography cytology is commonly performed in these patients; however, its sensitivity for diagnosis of HPB malignancy is poor (41.6%). Many adjunctive tests have been investigated to improve the sensitivity of HPB biopsies. To determine the best tests available, however, we reviewed the literature and performed a comparative analysis of all recently investigated tests and their sensitivities. METHODS A PubMed search identified articles published between 2003 and 2014, describing alternate methods for diagnosing HPB malignancies, reported sensitivity, final pathology, and had data available online. Meta-analysis was conducted for tests with multiple articles. Tests with the highest sensitivity and specificities were reported. RESULTS A total of 77 studies were identified. Meta-analysis was performed on the sensitivity of EUS-FNA (74.2%), fluorescence in situ hybridization (54.2%), immunostain of insulin-like growth factor 2 mRNA-binding Protein 3 (IMP3; 80.4%), IMP3 + cytology (86.4%), K homology domain containing protein overexpressed in cancer (KOC; 85.9%), S100P (77.8%), serum CA19-9 (69.3%), and K-ras mutations (47.0%) to detect malignancy. Ultimately, 12 tests were identified with superior sensitivity (85.3%-100%) and specificities (81.6%-100%) including stricture scrapping, brush sectioning, IMP3 stain + cytology, IMP3+S100A4, bile carcinoembryonic cell adhesion molecule 6 protein (±CA19-9), bile micro RNA (miRNA)-135b, serum miRNA-RNU2-1f, serum miRNA-21 (+CA19-9), peripheral blood mononuclear cells miRNA-27a-3p (+CA19-9), serum miRNA-16 + miRNA-196a (+CA19-9), peripheral blood mononuclear cells mRNAs h-TERT + CK20 + CEA + C-MET. CONCLUSIONS We recommend immunostaining with a panel of IMP3+KOC + S100A4 + cytology to achieve maximum sensitivity and specificity from HPB biopsies. One biliary protein (carcinoembryonic cell adhesion molecule 6) and several RNAs (bile and blood) offer exceptional sensitivity and specificity and should be tested prospectively in larger populations. Overall, this review identifies several tests to improve the sensitivity of diagnostic algorithms to identify HPB malignancies.
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25
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Chen D, Huang JF, Xia H, Duan GJ, Chuai ZR, Yang Z, Fu WL, Huang Q. High-sensitivity PCR method for detecting BRAF V600E mutations in metastatic colorectal cancer using LNA/DNA chimeras to block wild-type alleles. Anal Bioanal Chem 2014; 406:2477-87. [PMID: 24500755 DOI: 10.1007/s00216-014-7618-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/27/2013] [Accepted: 01/07/2014] [Indexed: 01/15/2023]
Abstract
The response to epidermal growth factor receptor (EGFR)-targeted therapy in metastatic colorectal cancer (mCRC) is variable because of intra-tumor heterogeneity at the genetic level, and consequently, it is important to develop sensitive and selective assays to predict patient responses to therapy. Low-abundance BRAF V600E mutations are associated with poor response to treatment with EGFR inhibitors. We developed a method for the detection of BRAF V600E mutations in mCRC using real-time wild-type blocking PCR (WTB-PCR), in which a chimera composed of locked nucleic acids and DNA is incorporated to amplify the mutant allele at high efficiency while simultaneously inhibiting the amplification of wild-type alleles. Mixing experiments showed that this method is exquisitely sensitive, with detection of the mutated allele at a mutant/wild-type ratio of 1:10,000. To demonstrate the applicability of this approach for mCRC patients, we assessed the V600E mutations in 50 clinical cases of mCRC by real-time WTB-PCR. The percentage of patients with V600E mutation as determined by WTB-PCR (16%, 8/50) was higher than by traditional PCR (10%, 5/50), suggesting an increased sensitivity for WTB-PCR. By calculating the ΔC q for real-time traditional PCR, which amplifies all BRAF alleles, versus WTB-PCR, which selectively amplifies mutant BRAF, we demonstrated that among the V600E-positive mCRC patient samples, the percentage of BRAF DNA with the V600E mutation ranged from 0.05 to 52.32%. In conclusion, WTB-PCR provides a rapid, simple, and low-cost method to detect trace amounts of mutated BRAF V600E gene.
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Affiliation(s)
- Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
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de Biase D, Visani M, Baccarini P, Polifemo AM, Maimone A, Fornelli A, Giuliani A, Zanini N, Fabbri C, Pession A, Tallini G. Next generation sequencing improves the accuracy of KRAS mutation analysis in endoscopic ultrasound fine needle aspiration pancreatic lesions. PLoS One 2014; 9:e87651. [PMID: 24504548 PMCID: PMC3913642 DOI: 10.1371/journal.pone.0087651] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/27/2013] [Indexed: 02/05/2023] Open
Abstract
The use of endoscopic ultrasonography has allowed for improved detection and pathologic analysis of fine needle aspirate material for pancreatic lesion diagnosis. The molecular analysis of KRAS has further improved the clinical sensitivity of preoperative analysis. For this reason, the use of highly analytical sensitive and specific molecular tests in the analysis of material from fine needle aspirate specimens has become of great importance. In the present study, 60 specimens from endoscopic ultrasonography fine needle aspirate were analyzed for KRAS exon 2 and exon 3 mutations, using three different techniques: Sanger sequencing, allele specific locked nucleic acid PCR and Next Generation sequencing (454 GS-Junior, Roche). Moreover, KRAS was also tested in wild-type samples, starting from DNA obtained from cytological smears after pathological evaluation. Sanger sequencing showed a clinical sensitivity for the detection of the KRAS mutation of 42.1%, allele specific locked nucleic acid of 52.8% and Next Generation of 73.7%. In two wild-type cases the re-sequencing starting from selected material allowed to detect a KRAS mutation, increasing the clinical sensitivity of next generation sequencing to 78.95%. The present study demonstrated that the performance of molecular analysis could be improved by using highly analytical sensitive techniques. The Next Generation Sequencing allowed to increase the clinical sensitivity of the test without decreasing the specificity of the analysis. Moreover we observed that it could be useful to repeat the analysis starting from selectable material, such as cytological smears to avoid false negative results.
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Affiliation(s)
- Dario de Biase
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
- * E-mail:
| | - Michela Visani
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Paola Baccarini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Anna Maria Polifemo
- Unit of Gastroenterology, Azienda Unità Sanitaria Locale di Bologna - Bellaria Hospital, Bologna, Italy
| | | | - Adele Fornelli
- Anatomic Pathology Unit, Azienda Unità Sanitaria Locale di Bologna - Maggiore Hospital, Bologna, Italy
| | - Adriana Giuliani
- Indiana University, Bloomington, Indiana, United States of America
| | - Nicola Zanini
- Unit of General Surgery, Azienda Unità Sanitaria Locale di Bologna - Maggiore Hospital, Bologna, Italy
| | - Carlo Fabbri
- Unit of Gastroenterology, Azienda Unità Sanitaria Locale di Bologna - Bellaria Hospital, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
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Role of quantitative and qualitative characteristics of free circulating DNA in the management of patients with non-small cell lung cancer. Cell Oncol (Dordr) 2013; 36:439-48. [PMID: 24177991 DOI: 10.1007/s13402-013-0155-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The release of DNA into peripheral blood is a common event in cancer patients, occurring as a consequence of necrotic and apoptotic processes typical of tumor cells. However, free circulating DNA (fcDNA) is also present in patients with benign diseases and in healthy individuals. Both quantitative and qualitative aspects of fcDNA have been studied as potential biomarkers in a number of tumor types. In particular, quantitative analysis of fcDNA has been shown to play an important role in the diagnosis of non-small cell lung cancer (NSCLC), because of its ability to discriminate between healthy subjects and individuals with NSCLC. Additionally, fcDNA in cancer patients derives predominantly from tumor tissue and, as such, it can be used for the molecular characterization of the primary tumor. Targeted therapies in NSCLC have, in recent years, produced promising results, highlighting the importance of molecular profiling of the primary cancer lesions. Considering that little or no tumor material is available for at least some of the patients, the possibility of using fcDNA for molecular analysis becomes increasingly important. In the present review we evaluated several quantitative and qualitative aspects of fcDNA that could be instrumental for the differential diagnosis of lung disease. CONCLUSIONS There is ample evidence in the literature to support the possible use of peripheral blood-derived fcDNA in the early diagnosis and molecular characterization of lung cancer. This non-invasive method may also turn out to be valuable in monitoring drug response and in identifying induced mechanisms of drug resistance. Before it can be implemented in routine clinical practice, however, additional efforts are needed to standardize the methodology.
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Lin L, Weng S, Zhao C, Liu Q, liu A, Lin X. Hairpin LNA biosensor with enzyme tagged AuNPs as tracer for amperometric detection of K-ras mutation gene. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.07.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Masojć B, Górski B, van de Wetering T, Dębniak T, Cybulski C, Jakubowska A, Mędrek K, Rudnicka H, Dwight ZL, Lubiński J. Genotyping by Induced Förster Resonance Energy Transfer (iFRET) Mechanism and Simultaneous Mutation Scanning. Hum Mutat 2013; 34:iv. [DOI: 10.1002/humu.22281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Bohdan Górski
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
| | | | - Tadeusz Dębniak
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
| | - Krzysztof Mędrek
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
| | - Helena Rudnicka
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
| | | | - Jan Lubiński
- Department of Genetics and Pathology; Pomeranian Medical University; Szczecin; Poland
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Boiocchi L, Espinal-Witter R, Geyer JT, Steinhilber J, Bonzheim I, Knowles DM, Fend F, Orazi A. Development of monocytosis in patients with primary myelofibrosis indicates an accelerated phase of the disease. Mod Pathol 2013; 26:204-12. [PMID: 23018876 DOI: 10.1038/modpathol.2012.165] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Primary myelofibrosis is a type of chronic myeloproliferative neoplasm characterized by progressive bone marrow failure with worsening cytopenia and in a subset of patients, progression to acute leukemia. Published data in patients with myelodysplastic syndromes have shown that the development of monocytosis in the course of myelodysplastic syndromes is associated with a poor prognosis. A similar occurrence has been only sporadically reported in patients with primary myelofibrosis. Over a period of four years we identified 10 out of 237 cases of primary myelofibrosis who developed persistent absolute monocytosis (>1 × 10(9)/l) during the course of disease (5 men and 5 women; median age/range: 68 years/52-82). Monocytosis developed at a median interval of 42 months from diagnosis (range: 1-180) and persisted for a median period of 23 months (range: 2-57). Five patients died after developing monocytosis (range: 20-188 months) and two experienced worsening disease and became transfusion dependent. Monocytosis was associated with increased white blood cells, decreased hemoglobin, decreased platelet count, and the presence of circulating blasts. In three cases, bone marrow biopsies after the onset of monocytosis showed marked myelomonocytic proliferation with morphological shifting from a typical primary myelofibrosis marrow appearance to aspects compatible with an overt 'secondary' chronic myelomonocytic leukemia. Before the development of monocytosis, 5 of 10 patients carried the JAK2V617F mutation; five patients showed karyotypic alterations. No change in JAK2 mutational status or cytogenetic evolution were associated with the development of monocytosis. Four of nine patients analyzed showed KRAS mutation in codon 12 or 13 with low allele burden. This is the first study correlating monocytosis developing in primary myelofibrosis patients with bone marrow morphology, laboratory data, molecular analysis and clinical follow-up. Development of monocytosis in patients with established primary myelofibrosis is associated with rapid disease progression and these patients should be considered as a high-risk group associated with short survival.
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Affiliation(s)
- Leonardo Boiocchi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College/New York Presbyterian Hospital, New York, NY 10065, USA
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Tsao KC, Chiou CC, Chen TL, Huang CG, Hsieh EF, Shih SR. Detection of low copies of drug-resistant influenza viral gene by a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2012; 47:254-6. [PMID: 23266238 DOI: 10.1016/j.jmii.2012.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 07/17/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
Abstract
Influenza virus infection causes endemics almost yearly and pandemics occasionally. Although antivirals are available for the clinical treatment of influenza virus infection, the emergence of a drug-resistant virus has reduced the effectiveness of therapy and prophylaxis. Therefore, the timely detection of drug-resistant influenza viruses is important. A single-tube reaction using peptide nucleic acid (PNA) as both a polymerase chain reaction (PCR) clamp and a sensor probe was established to detect the low numbers of copies of viral genes that carry the resistant marker. Influenza A H1N1 viruses resistant to a clinically used antiviral, amantadine, are selected for the experimental design. The PNA-mediated reverse transcription-PCR detected 10 copies/μL of RNA from the resistant strain among 2 × 10(4) copies/μL of RNA from the sensitive strain. A rapid and sensitive method was established for detecting low numbers of drug-resistant genes of the influenza virus. The assay would help to monitorthe emergence of adrug-resistant influenza virus.
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Affiliation(s)
- Kuo-Chien Tsao
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Clinical Virology Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Long Chen
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Clinical Virology Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Erh-Fang Hsieh
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Clinical Virology Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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32
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Zhao J, Xie F, Zhong W, Wu W, Qu S, Gao S, Liu L, Zhao J, Wang M, Zhou J, Jie H, Chen W. Restriction endonuclease-mediated real-time digestion-PCR for somatic mutation detection. Int J Cancer 2012. [PMID: 23180674 DOI: 10.1002/ijc.27968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PCR is a powerful platform for clinical and diagnostic applications, but challenges remain in detecting somatic mutations, as mutant cells are often mixed with more numerous wild-type cells at the tissue-sample sites. Here, we describe a novel method that couples PCR with restriction endonuclease digestion (designated real-time digestion-PCR, or RTD-PCR) in a one-step reaction tube for detecting somatic mutations from a minority of cells. The PCR mixture contains a thermostable restriction enzyme that digests wild-type alleles during the PCR program, allowing selective amplification of the mutant alleles. To validate this method, we used real-time digestion-PCR for the specific detection of the EGFR (epidermal growth factor receptor) treatment resistance-inducing mutation, T790M, combining with three different platforms: Sanger sequencing, TaqMan probe PCR and Sequenom MassArray. From 78 clinical samples, seven T790M mutations were consistently detected on all three platforms, indicating that RTD-PCR may be a useful clinical tool for analyzing the T790M point mutation.
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Affiliation(s)
- Jinyin Zhao
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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Nogueira da Costa A, Herceg Z. Detection of cancer-specific epigenomic changes in biofluids: powerful tools in biomarker discovery and application. Mol Oncol 2012; 6:704-15. [PMID: 22925902 PMCID: PMC5528342 DOI: 10.1016/j.molonc.2012.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 07/30/2012] [Indexed: 01/30/2023] Open
Abstract
The genetic and epigenetic material originating from tumour that can be found in body fluids of individuals with cancer harbours tumour-specific alterations and represents an attractive target for biomarker discovery. Epigenetic changes (DNA methylation, histone modifications and non-coding RNAs) are present ubiquitously in virtually all types of human malignancies and may appear in early cancer development, and thus they provide particularly attractive markers with broad applications in diagnostics. In addition, because changes in the epigenome may constitute a signature of specific exposure to certain risk factors, they have the potential to serve as highly specific biomarkers for risk assessment. While reliable detection of cancer-specific epigenetic changes has proven to be technically challenging, a substantial progress has been made in developing the methodologies that allow an efficient and sensitive detection of epigenomic changes using the material originating from body fluids. In this review we discuss the application of epigenomics as a tool for biomarker research, with the focus on the analysis of DNA methylation in biofluids.
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Affiliation(s)
- André Nogueira da Costa
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon, Cedex 08, France
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Lin L, Liu A, Zhao C, Weng S, Lei Y, Liu Q, Lin X, Chen Y. A chronocoulometric LNA sensor for amplified detection of K-ras mutation based on site-specific DNA cleavage of restriction endonuclease. Biosens Bioelectron 2012; 42:409-14. [PMID: 23220265 DOI: 10.1016/j.bios.2012.09.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/30/2022]
Abstract
An amplified chronocoulometric Locked nucleic acid (LNA) sensor (CLS) for selective electrochemical detection of K-ras mutation was developed based on site-specific DNA cleavage of restriction endonuclease EcoRI. Thiolated-hairpin LNA probe with palindrome structure of stem was immobilized on the gold nanoparticles modified gold electrode (NG/AuE). It can be cleaved by EcoRI in the absence of K-ras mutation-type DNA (complementary with the loop part of hairpin probe), but cannot be cleaved in the presence of mutation-type DNA. The difference before and after enzymatic cleavage was then monitored by chronocoulometric biosensor. Electrochemical signals are generated by chronocoulometric interrogation of Hexaammineruthenium (III) chloride (RuHex) that quantitatively binds to surface-confined hairpin LNA probe via electrostatic interactions. The results suggested this CLS had a good specificity to distinguish the K-ras mutation-type, wild-type and non-complementary sequence. There was a good linear relationship between the charge and the logarithmic function of K-ras mutation-type DNA concentration. The detection limit had been estimated as 0.5 fM. It is possible to qualitatively and quantitatively detect K-ras point mutation in pancreatic cancer.
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Affiliation(s)
- Liqing Lin
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350004, China
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Dutta SK, Girotra M, Singla M, Dutta A, Otis Stephen F, Nair PP, Merchant NB. Serum HSP70: a novel biomarker for early detection of pancreatic cancer. Pancreas 2012; 41:530-4. [PMID: 22158074 PMCID: PMC4193547 DOI: 10.1097/mpa.0b013e3182374ace] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Heat shock protein 70 (HSP70) is overexpressed in human pancreatic cancer cell lines. To determine if serum HSP70 levels are elevated in patients with pancreatic cancer and can function as a biomarker for early detection of pancreatic cancer. METHODS Study subjects were divided into 3 groups: histologically proven pancreatic cancer (PC; n = 23), chronic pancreatitis (CP; n = 12), and matched normal control subjects (C; n = 10). Serum HSP70 levels were determined using a novel immunoelectrophoresis method developed and validated by the authors. Significance of difference between the groups was analyzed with analysis of variance (ANOVA). Receiver operating characteristic (ROC) curve analysis was performed to discriminate patients with pancreatic cancer from normal controls. RESULTS The mean ± SE serum HSP70 levels in the PC, CP, and C groups were 1.68 ± 0.083 ng/mL, 0.40 ± 0.057 ng/mL, and 0.04 ng/mL, respectively. Serum HSP70 levels in the PC group were significantly higher compared with either the CP or C groups (P < 0.01). The sensitivity and specificity of elevated serum HSP70 in the PC group was 74% and 90%, respectively. CONCLUSIONS Serum HSP70 levels are significantly increased in patients with pancreatic cancer and may be useful as an additional biomarker for the detection of pancreatic cancer.
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Affiliation(s)
- Sudhir K Dutta
- Division of Gastroenterology, University of Maryland School of Medicine, Sinai Hospital of Baltimore, Baltimore, MD 21215, USA.
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Yu S, Wu J, Xu S, Tan G, Liu B, Feng J. Modified PNA-PCR method: a convenient and accurate method to screen plasma KRAS mutations of cancer patients. Cancer Biol Ther 2012; 13:314-20. [PMID: 22310974 DOI: 10.4161/cbt.19075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
KRAS mutations are proved to confer dramatic resistance to EGFR target therapy of cancer patients. The aim of this study was to establish a convenient and accurate method to screen plasma KRAS mutations of cancer patients since tumor specimens were not always available in clinical practice. A modified PNA-PCR method was established and evaluated in plasma of 19 pancreatic cancer patients. Our results showed that the modified PNA-PCR assay was a sensitive (87.5%, 14/16) and accurate (92.9%, 13/14) method to screen plasma KRAS mutations of pancreatic cancer patients and there was a high consistency of KRAS mutation status between plasma samples and tumor specimens. The modified protocol could not only screen plasma KRAS mutations rapidly and accurately but also had potential to quantify KRAS mutant DNA to predict treatment response of cancer patients and monitor disease progression. It's should be indicated that this modified assay was only confirmed in the pancreatic cancer patients in this study and need to be verified in other cancer patients.
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Affiliation(s)
- Shaorong Yu
- Department of Medical Oncology, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
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K-ras mutations in the plasma correspond to computed tomographic findings in patients with pancreatic cancer. Pancreas 2012; 41:323-5. [PMID: 22044911 DOI: 10.1097/mpa.0b013e3182289118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Traditional approaches to sequence analysis are widely used to guide therapy for patients with lung and colorectal cancer and for patients with melanoma, sarcomas (eg, gastrointestinal stromal tumor), and subtypes of leukemia and lymphoma. The next-generation sequencing (NGS) approach holds a number of potential advantages over traditional methods, including the ability to fully sequence large numbers of genes (hundreds to thousands) in a single test and simultaneously detect deletions, insertions, copy number alterations, translocations, and exome-wide base substitutions (including known "hot-spot mutations") in all known cancer-related genes. Adoption of clinical NGS testing will place significant demands on laboratory infrastructure and will require extensive computational expertise and a deep knowledge of cancer medicine and biology to generate truly useful "clinically actionable" reports. It is anticipated that continuing advances in NGS technology will lower the overall cost, speed the turnaround time, increase the breadth of genome sequencing, detect epigenetic markers and other important genomic parameters, and become applicable to smaller and smaller specimens, including circulating tumor cells and circulating free DNA in plasma.
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Affiliation(s)
- Jeffrey S. Ross
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY
- Foundation Medicine, Cambridge, MA
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Cronin M, Ross JS. Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology. Biomark Med 2011; 5:293-305. [PMID: 21657839 DOI: 10.2217/bmm.11.37] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA sequence analysis has become a significant laboratory test in oncology, permitting treatment to become increasingly personalized for both solid tumors and hematologic malignancies. Traditional approaches to sequence analysis, including Sanger sequencing, pyrosequencing and allele-specific PCR, are now widely used to guide therapy for patients diagnosed with lung and colorectal cancer as well as for melanoma, sarcomas (e.g., gastrointestinal stromal tumors) and subtypes of leukemia and lymphoma. Traditional sequence analysis has been limited in bandwidth and throughput and as a result, has been focused exclusively on testing the most common aberrations in key genes or fully sequencing single genes. The massively parallel or next-generation sequencing (NGS) approach to DNA analysis holds a number of potential advantages over the traditional methods, including the ability to fully sequence large numbers of genes (hundreds to thousands) in a single test. Furthermore, NGS can simultaneously detect deletions, insertions, copy number alterations, translocations and exome-wide base substitutions (including known hot-spot mutations) in all known cancer-related genes. However, significant challenges, particularly with respect to demands on expertise and infrastructure, will have to be overcome to translate NGS to the bedside of the cancer patient. Extensive computational expertise is required to bring NGS into clinical context, and a deep knowledge of cancer medicine and cancer biology will be required to generate truly useful, so-called 'clinically actionable' reports for clinicians. While NGS is on the cusp of being launched as a clinical test, it may be expected that the near future will continue to bring major advances in the technology that will lower the overall cost, speed up the turnaround time, increase the breadth of genome sequencing, and detect epigenetic markers and other important genomic parameters, while becoming applicable to smaller and smaller specimens, including circulating tumor cells and circulating free DNA in plasma.
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Chen Z, Duldulao MP, Li W, Lee W, Kim J, Garcia-Aguilar J. Molecular diagnosis of response to neoadjuvant chemoradiation therapy in patients with locally advanced rectal cancer. J Am Coll Surg 2011; 212:1008-1017.e1. [PMID: 21458303 PMCID: PMC3104075 DOI: 10.1016/j.jamcollsurg.2011.02.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 02/11/2011] [Accepted: 02/22/2011] [Indexed: 02/06/2023]
Abstract
BACKGROUND Pathologic complete response (pCR) to neoadjuvant chemoradiation (CRT) is an important prognostic factor in locally advanced rectal cancer. However, it is uncertain if histopathological techniques accurately detect pCR. We tested a novel molecular approach for detecting pCR and compared it with current histopathological approaches. STUDY DESIGN Pretreatment tumor biopsies and surgical specimens were collected from 96 patients with locally advanced rectal cancer treated with neoadjuvant CRT and surgery. Tumor response was categorized by tumor regression grade. Tumor DNA from pre-CRT tumor biopsies was screened for K-ras and p53 mutations. DNA from paired surgical specimens was then screened for the same mutations using highly sensitive polymerase chain reaction-based techniques. RESULTS Sixty-eight of 96 (71%) pretreatment biopsies harbored K-ras and/or p53 mutation; 36 (38%) had K-ras mutations, 52 (54%) had p53 mutations, and 20 (21%) carried both mutations. Of 70 patients with tumor regression grades 1 to 3, sixty-six (94%) had a concordant K-ras and p53 mutation profile in pre- and post-treatment tissues. Of 26 patients with tumor regression grade 0 (pCR), 12 had K-ras or p53 mutations in pretreatment biopsies. Of these, 2 (17%) patients had the same K-ras (n = 1) or p53 (n = 1) mutation detected in post-treatment tissue. CONCLUSIONS Sensitive molecular techniques detect K-ras and p53 mutations in post-CRT surgical specimens in some patients with a pCR. This suggests histopathological techniques might not be completely accurate, and some patients diagnosed with a pCR to CRT might have occult cancers cells in their surgical specimens.
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Affiliation(s)
- Zhenbin Chen
- Department of Surgery, City of Hope, Duarte, CA, USA
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41
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Rare allele enrichment and detection by allele-specific PCR, competitive probe blocking, and melting analysis. Biotechniques 2011. [DOI: 10.2144/000113668] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Differential amplification of variant and wild-type alleles by PCR is often used for rare allele enrichment. We have combined allele-specific PCR, competitive probe blocking, asymmetric PCR, and melting analysis to enhance rare allele detection in a homogeneous system. Unlabeled, dual hybridization or molecular beacon probes were used for competitive blocking of the wild-type allele at a concentration 10 times that of the allele-specific primer. In each case, rare alleles were detected by probe melting analysis at a sensitivity of >0.001% (1 variant copy within 100,000 wild-type copies), providing single copy detection in typical PCRs. Ninety-one thyroid biopsies were tested for the BRAF mutation p.V600E (c.1799 T > A) by both dual hybridization probes without enrichment and an allele-specific, competitive blocking melting analysis with unlabeled probes. Eighty-seven samples were concordant between methods (43 positive, 44 negative), while 4 samples that were negative by direct analysis became positive after enrichment. Probes that both block wild-type amplification and detect rare variants by melting analysis improve the detection sensitivity of allele-specific PCR for rare alleles. In particular, melting analysis using unlabeled probes and amplification by rapid-cycle PCR provides cost-effective and fast enrichment and detection of rare alleles.
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Kitano S, Nakayama M, Yamane A, Tsukahara Y, Amano M. Detection of DNA mutations by fluorescence resonance energy transfer-based preferential homoduplex formation assay. Anal Biochem 2011; 408:197-205. [DOI: 10.1016/j.ab.2010.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/18/2010] [Accepted: 09/08/2010] [Indexed: 11/25/2022]
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Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker--a critical appraisal of the literature. Clin Chim Acta 2010; 411:1611-24. [PMID: 20688053 DOI: 10.1016/j.cca.2010.07.032] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/24/2010] [Accepted: 07/25/2010] [Indexed: 12/21/2022]
Abstract
Circulating cell-free DNA (cfDNA) has been suggested as a cancer biomarker. Several studies assessed the usefulness of quantitative and qualitative tumor-specific alterations of cfDNA, such as DNA strand integrity, frequency of mutations, abnormalities of microsatellites, and methylation of genes, as diagnostic, prognostic, and monitoring markers in cancer patients. Most of the papers that could be evaluated in this review resulted in a positive conclusion. However, methodical diversity without the traceability of data and differently designed and often underpowered studies resulted in divergent results between studies. In addition, the limited diagnostic sensitivity and specificity of cfDNA alterations temper the effusive hope of novel tumor markers, raising similar issues as those for other tumor markers. To validate the actual clinical validity of various cfDNA alterations as potential cancer biomarkers in practice for individual tumor types, the main problems of the observed uncertainties must be considered in future studies. These include methodical harmonization concerning sample collection, processing, and analysis with the traceability of measurement results as well as the realization of well-designed prospective studies based on power analysis and sample size calculations.
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Affiliation(s)
- Klaus Jung
- Department of Urology, Research Division, University Hospital Charité, Schumannstr. 20/21, 10117 Berlin, Germany.
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44
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Mutational analysis of K-ras codon 12 in blood samples of patients with acute myeloid leukemia. Leuk Res 2010; 34:883-91. [DOI: 10.1016/j.leukres.2010.02.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 02/02/2010] [Accepted: 02/22/2010] [Indexed: 11/17/2022]
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Detection of Occult Metastases in Sentinel Lymph Nodes From Colon Cancer Patients by K-ras Mutation Peptide Nucleic Acid Clamp PCR. Ann Surg 2010; 251:1087-91. [DOI: 10.1097/sla.0b013e3181dae1bc] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Oh JE, Lim HS, An CH, Jeong EG, Han JY, Lee SH, Yoo NJ. Detection of low-level KRAS mutations using PNA-mediated asymmetric PCR clamping and melting curve analysis with unlabeled probes. J Mol Diagn 2010; 12:418-24. [PMID: 20413678 DOI: 10.2353/jmoldx.2010.090146] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Detection of somatic mutations in clinical cancer specimens is often hampered by excess wild-type DNA. The aim of this study was to develop a simple and economical protocol without using fluorescent probes to detect low-level mutations. In this study, we combined peptide nucleic acid (PNA)-clamping PCR with asymmetric primers and a melting curve analysis using an unlabeled detection probe. PNA-clamping PCR, which suppressed amplification of the wild-type allele, was more sensitive for KRAS codon 12 mutation detection than nonclamping PCR in 5 different mutant cell lines. Three detection probes were tested (a perfectly matched antisense, a mismatched antisense, and a mismatched sense), and the mismatched sense detection probe showed the highest sensitivity (0.1% mutant detection) under clamping conditions. With this probe, we were able to detect not only the perfectly matched KRAS mutation, but also 4 other mismatched mutations of KRAS. We then applied this protocol to 10 human colon cancer tissues with KRAS codon 12 mutations, successfully detecting the mutations in all of them. Our data indicate that the combination of perfectly matched antisense PNA and a mismatched sense detection probe can detect KRAS mutations with a high sensitivity in both cell lines and human tissues. Moreover, this study might prove an easily applicable protocol for the detection of low-level mutations in other cancer genes.
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Affiliation(s)
- Ji Eun Oh
- Department of Pathology, College of Medicine, Catholic University of Korea, 505 Banpo-dong, Socho-gu, Seoul 137-701, Korea
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47
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Zhou L, Palais RA, Smith GD, Anderson D, Rowe LR, Wittwer CT. Enrichment and detection of rare alleles by means of snapback primers and rapid-cycle PCR. Clin Chem 2010; 56:814-22. [PMID: 20299678 DOI: 10.1373/clinchem.2009.142034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Selective amplification of minority alleles is often necessary to detect cancer mutations in clinical samples. METHODS Minor-allele enrichment and detection were performed with snapback primers in the presence of a saturating DNA dye within a closed tube. A 5' tail of nucleotides on 1 PCR primer hybridizes to the variable locus of its extension product to produce a hairpin that selectively enriches mismatched alleles. Genotyping performed after rapid-cycle PCR by melting of the secondary structure identifies different variants by the hairpin melting temperature (T(m)). Needle aspirates of thyroid tissue (n = 47) and paraffin-embedded biopsy samples (n = 44) were analyzed for BRAF (v-raf murine sarcoma viral oncogene homolog B1) variant p.V600E, and the results were compared with those for dual hybridization probe analysis. Needle aspirates of lung tumors (n = 8) were analyzed for EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] exon 19 in-frame deletions. RESULTS Use of 18-s cycles and momentary extension times of "0 s" with rapid-cycle PCR increased the selective amplification of mismatched alleles. A low Mg(2+) concentration and a higher hairpin T(m) relative to the extension temperature also improved the detection limit of mismatched alleles. The detection limit was 0.1% for BRAF p.V600E and 0.02% for EGFR exon 19 in-frame deletions. Snapback and dual hybridization probe methods for allele quantification of the thyroid samples correlated well (R(2) = 0.93) with 2 more BRAF mutations (45 and 43, respectively, of 91 samples) detected after snapback enrichment. Different EGFR in-frame deletions in the lung samples produced different hairpin T(m)s. CONCLUSIONS Use of snapback primers for enrichment and detection of minority alleles is simple, is inexpensive to perform, and can be completed in a closed tube in <25 min.
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Affiliation(s)
- Luming Zhou
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA.
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48
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Monzon FA, Ogino S, Hammond MEH, Halling KC, Bloom KJ, Nikiforova MN. The role of KRAS mutation testing in the management of patients with metastatic colorectal cancer. Arch Pathol Lab Med 2009; 133:1600-6. [PMID: 19792050 DOI: 10.5858/133.10.1600] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2009] [Indexed: 11/06/2022]
Abstract
CONTEXT KRAS mutations can be detected in approximately 30% to 40% of all patients with colorectal cancer. Several recent studies have shown that patients with KRAS mutations in codons 12 or 13 in metastatic tumors do not benefit from anti-epidermal growth factor receptor therapy with cetuximab or panitumumab. OBJECTIVE To review the literature on the role of KRAS mutation testing for management of patients with metastatic colorectal cancer and to discuss testing strategies. DATA SOURCES This review is based on published, peer-reviewed literature; available information from medical organizations (eg, National Comprehensive Cancer Network, American Society of Clinical Oncology, College of American Pathologists); and information from clinical laboratories conducting KRAS mutation analysis. CONCLUSIONS Multiple methods for detecting KRAS mutations in colorectal tumors are available, and all methods in current clinical use appear to have adequate clinical sensitivity for predicting a lack of response to cetuximab and panitumumab. Pathologist expertise is essential to quality KRAS testing and to determining effective treatment for patients with metastatic colorectal cancer.
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Affiliation(s)
- Federico A Monzon
- Department of Molecular Diagnostics, The Methodist Hospital Research Institute, Houston, Texas 77030-2703, USA.
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Duffy MJ, Sturgeon C, Lamerz R, Haglund C, Holubec VL, Klapdor R, Nicolini A, Topolcan O, Heinemann V. Tumor markers in pancreatic cancer: a European Group on Tumor Markers (EGTM) status report. Ann Oncol 2009; 21:441-447. [PMID: 19690057 DOI: 10.1093/annonc/mdp332] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the most difficult malignancies to diagnose and treat. The aim of this article is to review how tumor markers can aid the diagnosis and management of patients with this malignancy. The most widely used and best validated marker for pancreatic cancer is CA 19-9. Inadequate sensitivity and specificity limit the use of CA 19-9 in the early diagnosis of pancreatic cancer. In non-jaundiced patients, however, CA 19-9 may complement other diagnostic procedures. In patients with resectable pancreatic cancer, presurgical and postresection CA 19-9 levels correlate with overall survival. In advanced disease, elevated pretreatment levels of CA 19-9 are associated with adverse patient outcome and thus may be combined with other factors for risk stratification. Most, but not all, reports indicate that serial levels of CA 19-9 correlate with response to systemic therapy. Use of CA 19-9 kinetics in conjunction with imaging is therefore recommended in monitoring therapy. Although several potential serum and tissue markers for pancreatic cancer are currently undergoing evaluation, none are sufficiently validated for routine clinical use. CA 19-9 thus remains the serum pancreatic cancer marker against which new markers for this malignancy should be judged.
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Affiliation(s)
- M J Duffy
- Department of Pathology and Laboratory Medicine, St Vincent's University Hospital, Dublin; UCD School of Medicine and Medical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
| | - C Sturgeon
- Department of Clinical Biochemistry, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - R Lamerz
- Medical Klinik II, Klinikum Grosshadern, Munich, Germany
| | - C Haglund
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - V L Holubec
- Second Department of Internal Medicine, University Hospital, Pilsen, Czech Republic
| | - R Klapdor
- Centre for Clinical and Experimental Tumour Diagnosis and Therapy, Hamburg, Germany
| | - A Nicolini
- Department of Internal Medicine, University of Pisa, Pisa, Italy
| | - O Topolcan
- Second Department of Internal Medicine, University Hospital, Pilsen, Czech Republic
| | - V Heinemann
- Medical Clinic III, Klinikum Grosshadern, Munich, Germany
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50
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Follow-up study of K-ras mutations in the plasma of patients with pancreatic cancer: correlation with clinical features and carbohydrate antigen 19-9. Pancreas 2009; 38:534-41. [PMID: 19295453 DOI: 10.1097/mpa.0b013e31819f6376] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE We followed up the presence of Kirsten rat sarcoma (K-ras) mutations in plasma DNA and assessed its clinical value in patients with pancreatic cancer. METHODS Plasma samples (N = 430) of 56 patients with pancreatic cancer and 13 patients with pancreatitis were analyzed by real-time polymerase chain reaction using peptide nucleic acid-mediated polymerase chain reaction clamping. RESULTS K-ras mutations could be detected in the plasma DNA of 20 patients with cancer (36%). No K-ras mutation was found in the plasma of patients with pancreatitis. In 7 (35%) of 20 patients with lowly or moderately elevated carbohydrate antigen 19.9 (CA 19-9) levels lower than 100 U/mL, the result of the assay was positive for K-ras mutation. The combination of K-ras and CA 19-9 level determination gave a sensitivity for the diagnosis of pancreatic cancer of 91% (40/44) of the patients. Thirteen of 35 patients with pancreatic cancer (102 plasma samples) with elevated CA 19-9 levels (>35 U/mL) and altered K-ras gene showed significant correlation with elevated CA 19-9 levels (P=0.048). CONCLUSIONS The summary of our approach of noninvasive, convenient, extremely high-sensitive K-ras mutation analysis in plasma might provide diagnostic and prognostic information to clinicians but will not be sufficient in a standardized early diagnosis of pancreatic carcinoma. The combination with CA 19-9 assay is useful for detection and prognostic evaluation of pancreatic carcinoma.
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