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Eini M, Behzad-Behbahani A, Takhshid MA, Ramezani A, Rafiei Dehbidi GR, Okhovat MA, Farhadi A, Alavi P. Chimeric External Control to Quantify Cell Free DNA in Plasma Samples by Real Time PCR. Avicenna J Med Biotechnol 2016; 8:84-90. [PMID: 27141267 PMCID: PMC4842246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND DNA isolation procedure can significantly influence the quantification of DNA by real time PCR specially when cell free DNA (cfDNA) is the subject. To assess the extraction efficiency, linearity of the extraction yield, presence of co-purified inhibitors and to avoid problems with fragment size relevant to cfDNA, development of appropriate External DNA Control (EDC) is challenging. Using non-human chimeric nucleotide sequences, an EDC was developed for standardization of qPCR for monitoring stability of cfDNA concentration in blood samples over time. METHODS A0 DNA fragment of 167 bp chimeric sequence of parvovirus B19 and pBHA designated as EDC fragment was designed. To determine the impact of different factors during DNA extraction processing on quantification of cfDNA, blood samples were collected from normal subjects and divided into aliquots with and without specific treatment. In time intervals, the plasma samples were isolated. The amplicon of 167 bp EDC fragment in final concentration of 1.1 pg/500 μl was added to each plasma sample and total DNA was extracted by an in house method. Relative and absolute quantification real time PCR was performed to quantify both EDC fragment and cfDNA in extracted samples. RESULTS Comparison of real time PCR threshold cycle (Ct) for cfDNA fragment in tubes with and without specific treatment indicated a decrease in untreated tubes. In contrast, the threshold cycle was constant for EDC fragment in treated and untreated tubes, indicating the difference in Ct values of the cfDNA is because of specific treatments that were made on them. CONCLUSIONS Spiking of DNA fragment size relevant to cfDNA into the plasma sample can be useful to minimize the bias due to sample preparation and extraction processing. Therefore, it is highly recommended that standard external DNA control be employed for the extraction and quantification of cfDNA for accurate data analysis.
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Affiliation(s)
- Maryam Eini
- Department of Medical Biotechnology, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran,Corresponding author: Abbas Behzad-Behbahani, Ph.D., Diagnosis Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran, Tel: +98 71 32270301, Fax: +98 71 32270301 E-mail:,
| | - Mohammad Ali Takhshid
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences and Technology, Shiraz University of Medical Sciences, Shiraz, Iran,Institute for Cancer Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholam Reza Rafiei Dehbidi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Okhovat
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Farhadi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parniyan Alavi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Rossi E, Facchinetti A, Zamarchi R. Notes for developing a molecular test for the full characterization of circulating tumor cells. Chin J Cancer Res 2015; 27:471-8. [PMID: 26543333 DOI: 10.3978/j.issn.1000-9604.2015.09.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proved association between the circulating tumor cell (CTC) levels and the patients' survival parameters has been growing interest to investigate the molecular profile of these neoplastic cells among which hide out precursors capable of initiating a new distant metastatic lesion. The full characterization of the tumor cells in peripheral blood of cancer patients is expected to be of help for understanding and (prospectively) for counteracting the metastatic process. The major hitch that is hampering the successful gaining of this result is the lack of a consensus onto standard operating procedures (SOPs) for performing what we generally define as the "liquid biopsy". Here we review the more recent acquisitions in the analysis of CTCs and tumor related nucleic acids, looking to the main open questions that are hampering their definitive employ in the routine clinical practice.
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Affiliation(s)
- Elisabetta Rossi
- 1 Department of Surgery, Oncology and Gastroenterology, Oncology Section, University of Padova, Padova, Italy ; 2 IOV-IRCCS, Padova, Italy
| | - Antonella Facchinetti
- 1 Department of Surgery, Oncology and Gastroenterology, Oncology Section, University of Padova, Padova, Italy ; 2 IOV-IRCCS, Padova, Italy
| | - Rita Zamarchi
- 1 Department of Surgery, Oncology and Gastroenterology, Oncology Section, University of Padova, Padova, Italy ; 2 IOV-IRCCS, Padova, Italy
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203
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Bortolin MT, Tedeschi R, Bidoli E, Furlan C, Basaglia G, Minatel E, Gobitti C, Franchin G, Trovò M, De Paoli P. Cell-free DNA as a prognostic marker in stage I non-small-cell lung cancer patients undergoing stereotactic body radiotherapy. Biomarkers 2015; 20:422-8. [PMID: 26526078 DOI: 10.3109/1354750x.2015.1094139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To evaluate whether plasma cell-free DNA (cfDNA) was related to clinical outcome in inoperable stage I non-small cell lung cancer (NSCLC) patients undergoing stereotactic body radiotherapy (SBRT). MATERIALS AND METHODS Plasma cfDNA was assessed at baseline, before the last day and 45 days after the end of SBRT, in 22 NSCLC patients. Twenty-two healthy controls were also evaluated. RESULTS Plasma cfDNA was higher in patients than in controls. An association with unfavourable disease-free survival was found for continuous baseline cfDNA increments (HR = 5.9, 95%CI: 1.7-19.8, p = 0.04). CONCLUSION Plasma cfDNA may be a promising prognostic biomarker in high-risk NSCLC patients.
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Affiliation(s)
- Maria Teresa Bortolin
- a Microbiology-Immunology and Virology Unit, Oncology Reference Center, IRCCS , Aviano (PN) , Italy
| | - Rosamaria Tedeschi
- a Microbiology-Immunology and Virology Unit, Oncology Reference Center, IRCCS , Aviano (PN) , Italy
| | - Ettore Bidoli
- b Epidemiology and Biostatistic Unit, Oncology Reference Center, IRCCS , Aviano (PN) , Italy
| | - Carlo Furlan
- c Medical Radiotherapy Department, Oncology Reference Center, IRCCS , Aviano (PN) , Italy , and
| | - Giancarlo Basaglia
- a Microbiology-Immunology and Virology Unit, Oncology Reference Center, IRCCS , Aviano (PN) , Italy
| | - Emilio Minatel
- c Medical Radiotherapy Department, Oncology Reference Center, IRCCS , Aviano (PN) , Italy , and
| | - Carlo Gobitti
- c Medical Radiotherapy Department, Oncology Reference Center, IRCCS , Aviano (PN) , Italy , and
| | - Giovanni Franchin
- c Medical Radiotherapy Department, Oncology Reference Center, IRCCS , Aviano (PN) , Italy , and
| | - Marco Trovò
- c Medical Radiotherapy Department, Oncology Reference Center, IRCCS , Aviano (PN) , Italy , and
| | - Paolo De Paoli
- d Scientific Directorate, Oncology Reference Center, IRCCS , Aviano (PN) , Italy
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204
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Sillence KA, Roberts LA, Hollands HJ, Thompson HP, Kiernan M, Madgett TE, Welch CR, Avent ND. Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity than Real-time PCR. Clin Chem 2015; 61:1399-407. [PMID: 26354802 DOI: 10.1373/clinchem.2015.239137] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/24/2015] [Indexed: 11/06/2022]
Abstract
BACKGROUND Noninvasive genotyping of fetal RHD (Rh blood group, D antigen) can prevent the unnecessary administration of prophylactic anti-D to women carrying RHD-negative fetuses. We evaluated laboratory methods for such genotyping. METHODS Blood samples were collected in EDTA tubes and Streck® Cell-Free DNA™ blood collection tubes (Streck BCTs) from RHD-negative women (n = 46). Using Y-specific and RHD-specific targets, we investigated variation in the cell-free fetal DNA (cffDNA) fraction and determined the sensitivity achieved for optimal and suboptimal samples with a novel Droplet Digital™ PCR (ddPCR) platform compared with real-time quantitative PCR (qPCR). RESULTS The cffDNA fraction was significantly larger for samples collected in Streck BCTs compared with samples collected in EDTA tubes (P < 0.001). In samples expressing optimal cffDNA fractions (≥4%), both qPCR and digital PCR (dPCR) showed 100% sensitivity for the TSPY1 (testis-specific protein, Y-linked 1) and RHD7 (RHD exon 7) assays. Although dPCR also had 100% sensitivity for RHD5 (RHD exon 5), qPCR had reduced sensitivity (83%) for this target. For samples expressing suboptimal cffDNA fractions (<2%), dPCR achieved 100% sensitivity for all assays, whereas qPCR achieved 100% sensitivity only for the TSPY1 (multicopy target) assay. CONCLUSIONS qPCR was not found to be an effective tool for RHD genotyping in suboptimal samples (<2% cffDNA). However, when testing the same suboptimal samples on the same day by dPCR, 100% sensitivity was achieved for both fetal sex determination and RHD genotyping. Use of dPCR for identification of fetal specific markers can reduce the occurrence of false-negative and inconclusive results, particularly when samples express high levels of background maternal cell-free DNA.
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Affiliation(s)
- Kelly A Sillence
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Llinos A Roberts
- Department of Fetal Medicine, Plymouth Hospitals National Health Service Trust, Plymouth, UK
| | - Heidi J Hollands
- Department of Fetal Medicine, Plymouth Hospitals National Health Service Trust, Plymouth, UK
| | - Hannah P Thompson
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Michele Kiernan
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Tracey E Madgett
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - C Ross Welch
- Department of Fetal Medicine, Plymouth Hospitals National Health Service Trust, Plymouth, UK
| | - Neil D Avent
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK;
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205
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Lewis JM, Heineck DP, Heller MJ. Detecting cancer biomarkers in blood: challenges for new molecular diagnostic and point-of-care tests using cell-free nucleic acids. Expert Rev Mol Diagn 2015; 15:1187-200. [PMID: 26189641 DOI: 10.1586/14737159.2015.1069709] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As we move into the era of individualized cancer treatment, the need for more sophisticated cancer diagnostics has emerged. Cell-free (cf) nucleic acids (cf-DNA, cf-RNA) and other cellular nanoparticulates are now considered important and selective biomarkers. There is great hope that blood-borne cf-nucleic acids can be used for 'liquid biopsies', replacing more invasive tissue biopsies to analyze cancer mutations and monitor therapy. Conventional techniques for cf-nucleic acid biomarker isolation from blood are generally time-consuming, complicated and expensive. They require relatively large blood samples, which must be processed to serum or plasma before isolation of biomarkers can proceed. Such cumbersome sample preparation also limits the widespread use of powerful, downstream genomic analyses, including PCR and DNA sequencing. These limitations also preclude rapid, point-of-care diagnostic applications. Thus, new technologies that allow rapid isolation of biomarkers directly from blood will permit seamless sample-to-answer solutions that enable next-generation point-of-care molecular diagnostics.
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Affiliation(s)
- Jean M Lewis
- a 1 Department of Nanoengineering, University of California - San Diego, SME Building, 9500 Gilman Dr., La Jolla, CA 92093-0448, USA
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Abstract
The challenge of diagnosing childhood tuberculosis (TB) results from its paucibacillary nature and the difficulties of sputum collection in children. Mycobacterial culture, the diagnostic gold standard, provides microbiological confirmation in only 30% to 40% of childhood pulmonary TB cases and takes up to 6 weeks to result. Conventional drug susceptibility testing requires an additional 2 to 4 weeks after culture confirmation. In response to the low sensitivity and long wait time of the traditional diagnostic approach, many new assays have been developed. These new tools have shortened time to result; however, none of them offer greater sensitivity than culture.
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Affiliation(s)
- Silvia S Chiang
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA
| | - Douglas S Swanson
- Division of Infectious Diseases, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2401 Gillham Road, Kansas City, MO 64108, USA
| | - Jeffrey R Starke
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA.
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207
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Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma. Anal Bioanal Chem 2015; 407:6873-8. [DOI: 10.1007/s00216-015-8846-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/03/2015] [Accepted: 06/10/2015] [Indexed: 12/21/2022]
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208
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Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
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209
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Abstract
Many methods have been developed for DNA integrity assessment including electrophoresis-based procedures, quantitative PCR, and, more recently, microfluidics-based procedures. DNA integrity evaluation can be employed for characterizing biological samples quality before extensive genomic analysis and also finds applications in reproductive medicine, prenatal diagnostics, or cancer research. In this chapter, we will focus on the assessment of DNA integrity in cancer research. In particular, we will present the application of the determination of DNA integrity for tracking of circulating tumor DNA. Finally, we will conclude by illustrating the potential innovative application of DNA integrity as a biomarker in clinical research, especially for prognostic purposes, patient follow-up, or early diagnosis.
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210
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Devonshire AS, Honeyborne I, Gutteridge A, Whale AS, Nixon G, Wilson P, Jones G, McHugh TD, Foy CA, Huggett JF. Highly Reproducible Absolute Quantification of Mycobacterium tuberculosis Complex by Digital PCR. Anal Chem 2015; 87:3706-13. [DOI: 10.1021/ac5041617] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Alison S. Devonshire
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Isobella Honeyborne
- Centre
for Clinical Microbiology, Department of Infection, Royal Free Campus, University College London, London NW3 2PF, United Kingdom
| | - Alice Gutteridge
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Alexandra S. Whale
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Gavin Nixon
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Philip Wilson
- Statistics
Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Gerwyn Jones
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Timothy D. McHugh
- Centre
for Clinical Microbiology, Department of Infection, Royal Free Campus, University College London, London NW3 2PF, United Kingdom
| | - Carole A. Foy
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Jim F. Huggett
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
- Centre
for Clinical Microbiology, Department of Infection, Royal Free Campus, University College London, London NW3 2PF, United Kingdom
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211
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Abstract
Abstract
BACKGROUND
Targeted therapies have markedly changed the treatment of cancer over the past 10 years. However, almost all tumors acquire resistance to systemic treatment as a result of tumor heterogeneity, clonal evolution, and selection. Although genotyping is the most currently used method for categorizing tumors for clinical decisions, tumor tissues provide only a snapshot, or are often difficult to obtain. To overcome these issues, methods are needed for a rapid, cost-effective, and noninvasive identification of biomarkers at various time points during the course of disease. Because cell-free circulating tumor DNA (ctDNA) is a potential surrogate for the entire tumor genome, the use of ctDNA as a liquid biopsy may help to obtain the genetic follow-up data that are urgently needed.
CONTENT
This review includes recent studies exploring the diagnostic, prognostic, and predictive potential of ctDNA as a liquid biopsy in cancer. In addition, it covers biological and technical aspects, including recent advances in the analytical sensitivity and accuracy of DNA analysis as well as hurdles that have to be overcome before implementation into clinical routine.
SUMMARY
Although the analysis of ctDNA is a promising area, and despite all efforts to develop suitable tools for a comprehensive analysis of tumor genomes from plasma DNA, the liquid biopsy is not yet routinely used as a clinical application. Harmonization of preanalytical and analytical procedures is needed to provide clinical standards to validate the liquid biopsy as a clinical biomarker in well-designed and sufficiently powered multicenter studies.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
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212
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Redshaw N, Huggett JF, Taylor MS, Foy CA, Devonshire AS. Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis. BMC Genomics 2014; 15:1174. [PMID: 25539843 PMCID: PMC4523014 DOI: 10.1186/1471-2164-15-1174] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognostic biomarkers, however, there is currently a lack of consensus regarding the optimal methodologies to quantify methylation status. To address this issue we compared five analytical methods: (i) MethyLight qPCR, (ii) MethyLight digital PCR (dPCR), methylation-sensitive and -dependent restriction enzyme (MSRE/MDRE) digestion followed by (iii) qPCR or (iv) dPCR, and (v) bisulfite amplicon next generation sequencing (NGS). The techniques were evaluated for linearity, accuracy and precision. Results MethyLight qPCR displayed the best linearity across the range of tested samples. Observed methylation measured by MethyLight- and MSRE/MDRE-qPCR and -dPCR were not significantly different to expected values whilst bisulfite amplicon NGS analysis over-estimated methylation content. Bisulfite amplicon NGS showed good precision, whilst the lower precision of qPCR and dPCR analysis precluded discrimination of differences of < 25% in methylation status. A novel dPCR MethyLight assay is also described as a potential method for absolute quantification that simultaneously measures both sense and antisense DNA strands following bisulfite treatment. Conclusions Our findings comprise a comprehensive benchmark for the quantitative accuracy of key methods for methylation analysis and demonstrate their applicability to the quantification of circulating tumour DNA biomarkers by using sample concentrations that are representative of typical clinical isolates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1174) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jim F Huggett
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK.
| | - Martin S Taylor
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
| | - Carole A Foy
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK.
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Ilie M, Hofman V, Long E, Bordone O, Selva E, Washetine K, Marquette CH, Hofman P. Current challenges for detection of circulating tumor cells and cell-free circulating nucleic acids, and their characterization in non-small cell lung carcinoma patients. What is the best blood substrate for personalized medicine? ANNALS OF TRANSLATIONAL MEDICINE 2014; 2:107. [PMID: 25489581 DOI: 10.3978/j.issn.2305-5839.2014.08.11] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/13/2014] [Indexed: 12/29/2022]
Abstract
The practice of "liquid biopsy" as a diagnostic, prognostic and theranostic tool in non-small cell lung cancer (NSCLC) patients is an appealing approach, at least in theory, since it is noninvasive and easily repeated. In particular, this approach allows patient monitoring during treatment, as well as the detection of different genomic alterations that are potentially accessible to targeted therapy or are associated with treatment resistance. However, clinical routine practice is slow to adopt the liquid biopsy. Several reasons may explain this: (I) the vast number of methods described for potential detection of circulating biomarkers, without a consensus on the ideal technical approach; (II) the multiplicity of potential biomarkers for evaluation, in particular, circulating tumor cells (CTCs) vs. circulating tumor DNA (ctDNA); (III) the difficulty in controlling the pre-analytical phase to obtain robust and reproducible results; (IV) the present cost of the currently available techniques, which limits accessibility to patients; (V) the turnaround time required to obtain results that are incompatible with the urgent need for delivery of treatment. The purpose of this review is to describe the main advances in the field of CTC and ctDNA detection in NSCLC patients and to compare the main advantages and disadvantages of these two approaches.
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Affiliation(s)
- Marius Ilie
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Véronique Hofman
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Elodie Long
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Olivier Bordone
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Eric Selva
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Kevin Washetine
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Charles Hugo Marquette
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
| | - Paul Hofman
- 1 INSERM U1081/CNRS UMR7284, Team 3, University of Nice Sophia Antipolis, Antoine Lacassagne Cancer Center, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France ; 2 Human Biobank, 3 Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France ; 4 Cancer Research Association (ARC) Labelled Team, Villejuif, France ; 5 Department of Pneumology, Pasteur Hospital, Nice, France
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Huggett JF, Cowen S, Foy CA. Considerations for digital PCR as an accurate molecular diagnostic tool. Clin Chem 2014; 61:79-88. [PMID: 25338683 DOI: 10.1373/clinchem.2014.221366] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Digital PCR (dPCR) is an increasingly popular manifestation of PCR that offers a number of unique advantages when applied to preclinical research, particularly when used to detect rare mutations and in the precise quantification of nucleic acids. As is common with many new research methods, the application of dPCR to potential clinical scenarios is also being increasingly described. CONTENT This review addresses some of the factors that need to be considered in the application of dPCR. Compared to real-time quantitative PCR (qPCR), dPCR clearly has the potential to offer more sensitive and considerably more reproducible clinical methods that could lend themselves to diagnostic, prognostic, and predictive tests. But for this to be realized the technology will need to be further developed to reduce cost and simplify application. Concomitantly the preclinical research will need be reported with a comprehensive understanding of the associated errors. dPCR benefits from a far more predictable variance than qPCR but is as susceptible to upstream errors associated with factors like sampling and extraction. dPCR can also suffer systematic bias, particularly leading to underestimation, and internal positive controls are likely to be as important for dPCR as they are for qPCR, especially when reporting the absence of a sequence. SUMMARY In this review we highlight some of the considerations that may be needed when applying dPCR and discuss sources of error. The factors discussed here aim to assist in the translation of dPCR to diagnostic, predictive, or prognostic applications.
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Affiliation(s)
- Jim F Huggett
- LGC, Teddington, UK; Research Department of Infection, Division of Infection and Immunity, UCL, London, UK.
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Prognostic DNA methylation markers for prostate cancer. Int J Mol Sci 2014; 15:16544-76. [PMID: 25238417 PMCID: PMC4200823 DOI: 10.3390/ijms150916544] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC.
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