Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine

Day, Emerson; Dear, Paul H.; McCaughan, Frank

doi:10.1016/j.ymeth.2012.08.001

Cited by 170 publications

(140 citation statements)

References 65 publications

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“…ddPCR enables detection of multiple mutations (multiplexing) from the same sample. ddPCR has a high sensitivity [34][35][36][37], but it also has limitations in terms of small input DNA applicable for the individual assays. Aspects such as level of sensitivity, specificity and background remain subject to optimization in the development of specific assays.…”

Section: Methodsmentioning

confidence: 99%

Methodological, biological and clinical aspects of circulating free DNA in metastatic colorectal cancer

Spindler

2016

Acta Oncologica

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Background: Circulating DNA can be used to measure the total cell-free DNA (cfDNA) and for detection and quantification of tumor-specific genetic alterations in the peripheral blood, and the broad clinical potential of circulating DNA has attracted increasing focus over the past decade. Concentrations of circulating DNA are high in metastatic colorectal cancer (CRC), and the total levels of cfDNA have been reported to hold strong prognostic value. Colorectal tumors are characterized by a high frequency of well known, clinically relevant genetic alteration, which is readily detected in the cfDNA and holds potential for tailoring of palliative therapy and for monitoring during treatment. This review aims to present the current literature which has specifically reported data on the potential utility of cfDNA and on tumor-specific mutations in metastatic colorectal cancer (mCRC). Method: Methodological, biological and clinical aspects are discussed based on the most recent development in this specific setting, and eligible studies were identified by systematic literature searched from Pubmed and EMBASE in addition to conference papers and communications. Results: The literature regarding cfDNA in CRC is broad and heterogeneous concerning aims, nomenclature, methods, cohorts and clinical endpoints and consequently difficult to include in a single systematic search. However, the available data underline a strong clinical value of measuring both total cfDNA levels and tumor-specific mutations in the plasma of patients with mCRC, pre-and during systemic therapy. Conclusion: This paper had gathered the most recent literature on several aspects of cfDNA in mCRC, including methodological, biological and clinical aspects, and discussed the large clinical potential in this specific setting, which needs to be validated in carefully designed prospective studies in statistically relevant cohorts.

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Section: Methodsmentioning

confidence: 99%

Methodological, biological and clinical aspects of circulating free DNA in metastatic colorectal cancer

Spindler

2016

Acta Oncologica

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“…However, digital PCR still suffers from several disadvantages. [102][103][104] The copy numbers of different targets in a sample are often not known a priori and can vary by several orders of magnitude. Digital PCR quantification is most accurate at very low copy numbers, when estimates by Poisson statistics are not necessary.…”

Section: F Next Generation Sequencingmentioning

confidence: 99%

Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine

et al. 2016

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Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.

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“…Trotz der riesigen Auswahl an hochauflösenden Methoden scheinen sich digitale Verfahren durchzusetzen [49,50]. Die digitale PCR (dPCR) beruht auf ei- Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar.…”

Section: Hintergrundunclassified

Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA

Ulz

Geigl

Speicher

et al. 2016

Medizinische Genetik

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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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Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine

Cited by 170 publications

References 65 publications

Methodological, biological and clinical aspects of circulating free DNA in metastatic colorectal cancer

Methodological, biological and clinical aspects of circulating free DNA in metastatic colorectal cancer

Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine

Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA

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