An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection

Ou, Chen-Yin; Vu, Tam; Grunwald, Jonathan T.; Toledano, Michael; Zimak, Jan; Toosky, Melody N; Shen, Byron; Zell, Jason A.; Gratton, Enrico; Abram, Timothy J.; Zhao, Weian

doi:10.1039/c8lc01399c

Cited by 44 publications

(33 citation statements)

References 44 publications

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“…22 In 2016, the Cobas EGFR mutation Test v2 that interrogates by RT-PCR several mutations in exons 18, 19, 20 and 21 of epidermal growth factor receptor (EGFR) gene was the first liquid biopsy-based companion diagnostic to be approved by US Food and Drug Administration (FDA) and the European Medicines Agency for the prescription of EGFR inhibitors in patients with non-small-cell lung cancer (NSCLC) in cases when tumour biopsy tissue is not available. 23 Other targeted approaches, based mainly on digital PCR (droplet digital [ddPCR] or BEAMing dPCR), have been demonstrated to be able to detect specific known mutations, such as the main driver mutations of the primary tumour or variants associated with response to drugs in individual tumour types, and usually show high concordance with results obtained in tumour tissue [24][25][26] and reach a variant or mutant allele frequency detection (VAF/MAF) as low as 0.001% for the most advanced technologies 27 (i.e. the frequency of a particular genetic variation of a specific sequence [e.g.…”

Section: Mutations In Ctdnamentioning

confidence: 99%

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

et al. 2020

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Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes. Interestingly, however, cfDNA can also be used to analyse different features of DNA, such as methylation status, size fragment patterns, transcriptomics and viral load, which open new avenues for the analysis of liquid biopsy samples from cancer patients. This review will focus on the new perspectives and challenges of cfDNA analysis from mutation detection in patients with solid malignancies.

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Section: Mutations In Ctdnamentioning

confidence: 99%

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

et al. 2020

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“…In their approach, reverse transcription PCR and DMF technology were integrated for monitoring prostate cancer-related RNA from single-cell encapsulated droplets. ddPCR has been proven useful with numerous examples in the detection of circulating tumor DNA (ctDNA) in blood, urine and also solid tumor samples [26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41]. Joensson and coworkers integrated ddPCR with fluorescent color-coded Luminex®beads for multiplex detection of pathogen DNA biomarkers [42].…”

Section: Droplet-based Microfluidics For Genomicsmentioning

confidence: 99%

Recent Advances in Droplet-based Microfluidic Technologies for Biochemistry and Molecular Biology

2019

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Recently, droplet-based microfluidic systems have been widely used in various biochemical and molecular biological assays. Since this platform technique allows manipulation of large amounts of data and also provides absolute accuracy in comparison to conventional bioanalytical approaches, over the last decade a range of basic biochemical and molecular biological operations have been transferred to drop-based microfluidic formats. In this review, we introduce recent advances and examples of droplet-based microfluidic techniques that have been applied in biochemistry and molecular biology research including genomics, proteomics and cellomics. Their advantages and weaknesses in various applications are also comprehensively discussed here. The purpose of this review is to provide a new point of view and current status in droplet-based microfluidics to biochemists and molecular biologists. We hope that this review will accelerate communications between researchers who are working in droplet-based microfluidics, biochemistry and molecular biology.

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“…Thus, it seems to be more suitable to improve the cfDNA detection sensitivity based on ddPCR. Ou and colleagues [78] described an integrated comprehensive droplet digital detection (IC3D) digital PCR system (Figure 6). The system combined target-specific fluorescent chemistry, droplet microfluidics and a high-throughput 3D particle counting technology.…”

Section: Mutation Detection Of Cfdnamentioning

confidence: 99%

Microfluidic Technologies for cfDNA Isolation and Analysis

Qiao

2019

Micromachines

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Cell-free DNA (cfDNA), which promotes precision oncology, has received extensive concern because of its abilities to inform genomic mutations, tumor burden and drug resistance. The absolute quantification of cfDNA concentration has been proved as an independent prognostic biomarker of overall survival. However, the properties of low abundance and high fragmentation hinder the isolation and further analysis of cfDNA. Microfluidic technologies and lab-on-a-chip (LOC) devices provide an opportunity to deal with cfDNA sample at a micrometer scale, which reduces required sample volume and makes rapid isolation possible. Microfluidic platform also allow for high degree of automation and high-throughput screening without liquid transfer, where rapid and precise examination and quantification could be performed at the same time. Microfluidic technologies applied in cfDNA isolation and analysis are limited and remains to be further explored. This paper reviewed the existing and potential applications of microfluidic technologies in collection and enrichment of cfDNA, quantification, mutation detection and sequencing library construction, followed by discussion of future perspectives.

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An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection

Abstract: We present an ultra-sensitive, novel liquid biopsy approach which can uniquely enable detection of CTCs using genetic markers without pre-enrichment.

Cited by 44 publications

References 44 publications

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

Recent Advances in Droplet-based Microfluidic Technologies for Biochemistry and Molecular Biology

Microfluidic Technologies for cfDNA Isolation and Analysis

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