Influence of storage conditions and extraction methods on the quantity and quality of circulating cell-free DNA (ccfDNA): the SPIDIA-DNAplas External Quality Assessment experience

Malentacchi, Francesca; Pizzamiglio, Sara; Verderio, Paolo; Pazzagli, Mario; Orlando, Claudio; Ciniselli, Chiara Maura; Günther, Kalle; Gelmini, Stefania

doi:10.1515/cclm-2014-1161

Cited by 73 publications

(42 citation statements)

References 12 publications

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“…For diagnostic purposes, cfDNA must be extracted with kits or methods dedicated for cfDNA as use of generic DNA extraction methods will lead to a loss or further fragmentation of short cfDNA fragments . Extraction methods for cfDNA differ in several aspects (Figure ).…”

Section: Cfdna Extraction From Blood and Other Materialsmentioning

confidence: 99%

A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications

Volckmar

Sültmann

Riediger

et al. 2017

Genes Chromosomes & Cancer

167

151

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Recently, many genome-wide profiling studies provided insights into the molecular make-up of major cancer types. The deeper understanding of these genetic alterations and their functional consequences led to the discovery of novel therapeutic opportunities improving clinical management of cancer patients. While tissue-based molecular patient stratification is the gold standard for precision medicine, it has certain limitations: Tissue biopsies are invasive sampling procedures carrying the risk of complications and may not represent the entire tumor due to underlying genetic heterogeneity. In this context, complementary characterization of genetic information in the blood of cancer patients can serve as minimal-invasive 'liquid biopsy'. Fragments of circulating cell-free DNA (cfDNA) are released from tissues of healthy individuals as well as cancer patients. The fraction of cfDNA that is released from primary tumors or metastases (i.e. circulating tumor DNA, ctDNA) represents genetic aberrations in cancer cells, which are a potential source for diagnostic, prognostic, and predictive biomarkers. Recent studies have demonstrated technical feasibility and clinical applications including detection of drug targets and resistance mutations as well as longitudinal monitoring of tumors under therapy. To this end, a variety of pre-analytical procedures for blood processing, isolation and quantification of cfDNA are being employed and several analytical methods and technologies ranging from PCR-based single locus assays to genome-wide approaches are available, which considerably differ in sensitivity, specificity, and throughput. However, broad implementation of ctDNA analysis in daily clinical practice requires a thorough understanding of theoretical, technical, and biological concepts and necessitates standardization and validation of pre-analytical and analytical procedures across different technologies. Here, we review the pertinent literature and discuss the advantages and limitations of available methodologies and their potential applications in molecular diagnostics.

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Section: Cfdna Extraction From Blood and Other Materialsmentioning

confidence: 99%

A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications

Volckmar

Sültmann

Riediger

et al. 2017

Genes Chromosomes & Cancer

167

151

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“…These aspects include a number of pre-analytical parameters that can affect the concentration and fragmentation of cfDNA as recently discussed [24][25][26][27][28]. It seems that a reasonable level of consensus exists regarding the optimal source for cfDNA measurement as most studies suggest that quantification is more reliable when determined from plasma than from serum [24,25].…”

Section: Metastatic Colorectal Cancermentioning

confidence: 99%

“…The lack of direct comparison between studies and the numerous different quantification approaches renders progress in terms of clinical relevance difficult. Among others, the different nontumor-specific reference genes comprise cyclophilin, B2M, and albumin [26][27][28][31][32][33]; and other strategies include methylation assays or quantification of tumor-relevant genetic alterations [34]. Provided that all the above-mentioned steps are carefully considered, a reliable quantitative measure of total cfDNA is achievable and samples can be further analyzed to detect tumor-specific mutations and quantify the mutated alleles in the sample.…”

Section: Metastatic Colorectal Cancermentioning

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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“…First, our samples did not involve a cfDNA extraction process. Isolation of cfDNA from small amounts of plasma remains one of the greatest technical challenges that we still face with regard to ctDNA genotyping (36,37 ). However, it is nearly impossible for plasma to be used as a quality control material for ctDNA somatic mutation testing.…”

Section: Discussionmentioning

confidence: 99%

Synthetic Circulating Cell-free DNA as Quality Control Materials for Somatic Mutation Detection in Liquid Biopsy for Cancer

et al. 2017

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Influence of storage conditions and extraction methods on the quantity and quality of circulating cell-free DNA (ccfDNA): the SPIDIA-DNAplas External Quality Assessment experience

Abstract: The evidence-based results of the SPIDIA-DNAplas EQA have been proposed as a basis for the development of a Technical Specification by the European Committee for standardisation (CEN).

Cited by 73 publications

References 12 publications

A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications

A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications

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

Synthetic Circulating Cell-free DNA as Quality Control Materials for Somatic Mutation Detection in Liquid Biopsy for Cancer

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