Magnetic Nanowire Networks for Dual-Isolation and Detection of Tumor-Associated Circulating Biomarkers

Ampholytic ion-exchange magnetic beads: a promising tool for selecting short fragments in circulating cell-free DNA analysis

Objective

For liquid biopsy of cancer, the extraction of circulating cell-free DNA (cfDNA) from plasma is required. We evaluated the efficacy of use of magnetic submicron particles coated with abundant small zwitterions (MSP-ZEWBs) for extracting short fragments of cfDNA.

Methods

We developed and optimized an MSP-ZEWB-based cfDNA extraction method using ampholytic ion-exchange materials and compared its results with those using a control kit. We measured the cfDNA concentration by quantitative polymerase-chain-reaction and using the Qubit method and analyzed cfDNA fragmentation patterns using a bioanalyzer.

Results

The fragment size of cfDNA isolated from glycine hydrochloric acid at a pH of 2.2 exhibited a better alignment with the DNA marker. The highest DNA intensity was observed at the final concentration of 0.8% polyethylene glycol 8000. The intensity of cfDNA decreased significantly when isolated from plasma with DNA marker using MSP-ZEWBs with an adsorption buffer containing guanidine hydrochloride or isothiocyanoguanidine. All fragments were successfully extracted using MSP-ZEWBs from both plasma and phosphate-buffered saline. Notably, the intensity of short cfDNA fragments isolated using MSP-ZEWBs remained consistent for recovery of long DNA fragments. indicating a potential selective of small fragments.

Conclusion

The extraction of plasma cfDNA with MSP-ZEWBs requires no protein denaturation, shows resistance to cells remaining in plasma, and demonstrates higher overall efficiency and better reproducibility than other extraction methods. Use of MSP-ZEWBs may greatly enhance liquid biopsy of cancers through the analysis of plasma cfDNA in clinical practice.

Numerical Studies on the Motions of Magnetically Tagged Cells Driven by a Micromagnetic Matrix

Precisely controlling magnetically tagged cells in a complex environment is crucial to constructing a magneto-microfluidic platform. We propose a two-dimensional model for capturing magnetic beads from non-magnetic fluids under a micromagnetic matrix. A qualitative description of the relationship between the capture trajectory and the micromagnetic matrix with an alternating polarity configuration was obtained by computing the force curve of the magnetic particles. Three stages comprise the capture process: the first, where motion is a parabolic fall in weak fields; the second, where the motion becomes unpredictable due to the competition between gravity and magnetic force; and the third, where the micromagnetic matrix finally captures cells. Since it is not always obvious how many particles are adhered to the surface, attachment density is utilized to illustrate how the quantity of particles influences the capture path. The longitudinal magnetic load is calculated to measure the acquisition efficiency. The optimal adhesion density is 13%, and the maximum adhesion density is 18%. It has been demonstrated that a magnetic ring model with 100% adhesion density can impede the capture process. The results offer a theoretical foundation for enhancing the effectiveness of rare cell capture in practical applications.

A Targeted Exosome Therapeutic Confers Both CfDNA Scavenging and Macrophage Polarization for Ameliorating Rheumatoid Arthritis

Only a minority of rheumatoid arthritis (RA) patients achieve disease remission, so the exploration of additional pathogenic factors and the development of new therapeutics are needed. Here, strong correlations among the cell-free DNA (cfDNA) level and the inflammatory response in clinical synovial fluid samples and RA disease activity are discovered. The important role of cfDNA in disease development in a collagen-induced arthritis (CIA) murine model is also demonstrated. Building on these findings, a novel therapeutic based on anti-inflammatory (M2) macrophage-derived exosomes as chassis, that are modified with both oligolysine and matrix metalloproteinase (MMP)-cleavable polyethylene glycol (PEG) on the membrane, is developed. After intravenous injection, PEG-enabled prolonged circulation and C─C motif chemokine ligand-directed accumulation together result in enrichment at inflamed joints. Following subsequent MMP cleavage, the positively charged oligolysine is exposed for cfDNA scavenging, while exosomes induce M2 polarization. By using a classical CIA murine model and a newly established CIA canine model, it is demonstrated that the rationally designed exosome therapeutic substantially suppresses inflammation in joints and provides strong chondroprotection and osteoprotection, revealing its potential for effective CIA amelioration.

Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer

Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.

Magnetic enrichment of immuno-specific extracellular vesicles for mass spectrometry using biofilm-derived iron oxide nanowires

Immuno-specific enrichment of extracellular vesicles (EVs) can provide important information into cellular pathways underpinning various pathologies and for non-invasive diagnostics, including mass spectrometry-based analyses. Herein, we report an optimised protocol for immuno-magnetic enrichment of specific EV subtypes and their subsequent processing with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Specifically, we conjugated placental alkaline phosphatase (PLAP) antibodies to magnetic iron oxide nanowires (NWs) derived from bacterial biofilms and demonstrated the utility of this approach by enriching placenta-specific EVs (containing PLAP) from cell culture media. We demonstrate efficient PLAP+ve EV enrichment for both NW-PLAP and Dynabeads™-PLAP, with high PLAP protein recovery (83.7 ± 8.9% and 83.2 ± 5.9%, respectively), high particle-to-protein ratio (7.5 ± 0.7 × 10⁹ and 7.1 ± 1.2 × 10⁹, respectively), and low non-specific binding of non-target EVs (7 ± 3.2% and 5.4 ± 2.2%, respectively). Furthermore, our optimized EV enrichment and processing approach identified 2518 and 2545 protein groups with LC-MS/MS for NW-PLAP and Dynabead™-PLAP, respectively, with excellent reproducibility (Pearson correlation 0.986 and 0.988). These findings demonstrate that naturally occurring iron oxide NWs have comparable performance to current gold standard immune-magnetic beads. The optimized immuno-specific EV enrichment for LC-MS/MS method provides a low-cost and highly-scalable yet efficient, high-throughput approach for quality EV proteomic studies.

Nano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome

Over the past decade, the development of 'simple' blood tests that enable cancer screening, diagnosis or monitoring and facilitate the design of personalized therapies without the need for invasive tumour biopsy sampling has been a core ambition in cancer research. Data emerging from ongoing biomarker development efforts indicate that multiple markers, used individually or as part of a multimodal panel, are required to enhance the sensitivity and specificity of assays for early stage cancer detection. The discovery of cancer-associated molecular alterations that are reflected in blood at multiple dimensions (genome, epigenome, transcriptome, proteome and metabolome) and integration of the resultant multi-omics data have the potential to uncover novel biomarkers as well as to further elucidate the underlying molecular pathways. Herein, we review key advances in multi-omics liquid biopsy approaches and introduce the 'nano-omics' paradigm: the development and utilization of nanotechnology tools for the enrichment and subsequent omics analysis of the blood-circulating cancerome.

Direct Capture and Amplification of Small Fragmented DNAs Using Nitrogen-Mustard-Coated Microbeads

Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for "liquid biopsy" applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are complicated, and the extraction yield affects the precision of subsequent molecular diagnostic tests. Here, we report a novel approach using nitrogen-mustard-coated DNA capture beads (NMD beads) that covalently capture DNA and allow direct subsequent polymerase chain reaction (PCR) amplification from the NMD bead without elusion. The complex DNA extraction and purification processes are not required. To illustrate the diagnostic use of the NMD beads, we detected short DNA fragments (142 bp) that were spiked into fetal bovine serum (as a model serum sample). The spiked DNAs were captured directly from serum samples and detected using real-time PCR at concentrations as low as 10 fg/mL. We anticipate that this DNA capture bead technique has the potential to simplify the preanalytical processes required for cfDNA detection, which could significantly expand the diagnostic applications of liquid biopsy.

Early On-Treatment Prediction of the Mechanisms of Acquired Resistance to EGFR Tyrosine Kinase Inhibitors

BACKGROUND

Prediction of resistance mechanisms for epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) remains challenging. Thus, we investigated whether resistant cancer cells that expand shortly after EGFR-TKI treatment would eventually cause the resistant phenotype.

METHODS

We generated two EGFR-mutant lung cancer cell lines resistant to gefitinib (PC9GR and HCC827GR). The parent cell lines were exposed to short-term treatment with gefitinib or paclitaxel and then were assessed for EGFR T790M mutation and C-MET expression. These experiments were repeated in vivo and in clinically relevant patient-derived cell (PDC) models. For validation in clinical cases, we measured these gene alterations in plasma circulating tumor DNA (ctDNA) before and 8 weeks after starting EGFR-TKIs in four patients with EGFR-mutant lung cancer.

RESULTS

T790M mutation was only detected in the PC9GR cells, whereas C-MET amplification was detected in the HCC827GR cells. The T790M mutation level significantly increased in PC9 cells after short-term treatment with gefitinib but not in the paclitaxel. C-MET mRNA expression was only significantly increased in gefitinib-treated HCC827 cells. We confirmed that the C-MET copy number in HCC827 cells that survived after short-term gefitinib treatment was significantly higher than that in dead HCC827 cells. These findings were reproduced in the in vivo and PDC models. An early on-treatment increase in the plasma ctDNA level of these gene alterations was correlated with the corresponding resistance mechanism to EGFR-TKIs, a finding that was confirmed in post-treatment tumor tissues.

CONCLUSIONS

Early on-treatment kinetics in resistance-related gene alterations may predict the final mechanism of EGFR-TKI resistance.

Oxide nanowire microfluidics addressing previously-unattainable analytical methods for biomolecules towards liquid biopsy

Nanowire microfluidics using a combination of self-assembly and nanofabrication technologies is expected to be applied to various fields due to its unique properties. We have been working on the fabrication of nanowire microfluidic devices and the development of analytical methods for biomolecules using the unique phenomena generated by the devices. The results of our research are not just limited to the development of nanospace control with "targeted dimensions" in "targeted arrangements" with "targeted materials/surfaces" in "targeted spatial locations/structures" in microfluidic channels, but also cover a wide range of analytical methods for biomolecules (extraction, separation/isolation, and detection) that are impossible to achieve with conventional technologies. Specifically, we are working on the extraction technology "the cancer-related microRNA extraction method in urine," the separation technology "the ultrafast and non-equilibrium separation method for biomolecules," and the detection technology "the highly sensitive electrical measurement method." These research studies are not just limited to the development of biomolecule analysis technology using nanotechnology, but are also opening up a new academic field in analytical chemistry that may lead to the discovery of new pretreatment, separation, and detection principles.

Nanomaterials: Synthesis and Applications in Theranostics

Nanomaterials are endowed with unique features and essential properties suitable for employing in the field of nanomedicine. The nanomaterials can be classified as 0D, 1D, 2D, and 3D based on their dimensions. The nanomaterials can be malleable and ductile and they can be drawn into wires and sheets. Examples of nanomaterials are quantum dots (0D), nanorods, nanowires (1D), nanosheets (2D), and nanocubes (3D). These nanomaterials can be synthesized using top-down and bottom-up approaches. The achievements of 0D and 1D nanomaterials are used to detect trace heavy metal (e.g., Pb2+) and have higher sensitivity with the order of five as compared to conventional sensors. The achievements of 2D and 3D nanomaterials are used as diagnostic and therapeutic agents with multifunctional ability in imaging systems such as PET, SPECT, etc. These imaging modalities can be used to track the drug in living tissues. This review comprises the state-of-the-art of the different dimensions of the nanomaterials employed in theranostics. The nanomaterials with different dimensions have unique physicochemical properties that can be utilized for therapy and diagnosis. The multifunctional ability of the nanomaterials can have a distinct advantage that is used in the field of theranostics. Different dimensions of the nanomaterials would have more scope in the field of nanomedicine.

One-Step Polymerase Chain Reaction-Free Nanowire-Based Plasma Cell-Free DNA Assay to Detect EML4-ALK Fusion and to Monitor Resistance in Lung Cancer

BACKGROUND

Next-generation sequencing has mostly been used for genotyping cell-free DNA (cfDNA) in plasma. However, this assay has several clinical limitations. We evaluated the clinical utility of a novel polymerase chain reaction-free nanowire (NW)-based plasma cfDNA assay for detecting ALK fusion and mutations.

PATIENTS, MATERIALS, AND METHODS

We consecutively enrolled 99 patients with advanced non-small cell lung cancer undergoing a fluorescence in situ hybridization (FISH) test for ALK fusion; ALK-positive (n = 36). The NW-based assay was performed using 50-100 μL of plasma collected at pretreatment and every 8 weeks during ALK inhibitor treatment.

RESULTS

There was high concordance between the NW-based assay and the FISH test for identification of ALK fusion (94.9% with a kappa coefficient value of 0.892, 95% confidence interval [CI], 0.799-0.984). There was no difference in the response rate to the first anaplastic lymphoma kinase inhibitor between the ALK-positive patients identified by the NW-based assay and by the FISH test (73.5% vs. 72.2%, p = .931). In the ALK variant analysis, variants 1 and 3 subgroups were detected in 27 (75.0%) and 8 (22.2%) patients, respectively. Among 24 patients treated with crizotinib, variant 3 subgroup was associated with worse median overall survival than variant 1 subgroup (36.5 months; 95% CI, 0.09-87.6 vs. 19.8 months; 95% CI, 9.9-not reached, p = .004]. A serial assessment identified that ALK L1196M resistance mutation emerged before radiologic progression during crizotinib treatment.

CONCLUSION

The newly developed simple NW-based cfDNA assay may be clinically applicable for rapid diagnosis of ALK fusion with its variant forms and early detection of resistance.

IMPLICATIONS FOR PRACTICE

The authors developed a novel one-step polymerase chain reaction-free nanowire (NW)-based plasma cell-free DNA (cfDNA) assay. This study evaluated the clinical utility of this novel method for the diagnosis of EML4-ALK fusion in advanced non-small cell lung cancer (NSCLC). The NW-based assay and FISH test showed high concordance rate in 99 patients with advanced NSCLC. Serial cfDNA assessment demonstrated this method provided early detection of resistance before radiologic progression during crizotinib treatment. Taken together, plasma cfDNA genotyping by the NW-based cfDNA assay may be useful for the rapid diagnosis of ALK fusion, classifying variants, and early detection of resistance.

A nanowire-based liquid biopsy method using cerebrospinal fluid cell-free DNA for targeted management of leptomeningeal carcinomatosis

PURPOSE

This study aimed to evaluate whether genotyping cell free DNA (cfDNA) in the cerebrospinal fluid (CSF) may be helpful in managing leptomeningeal carcinomatosis (LMC) of EGFR-mutant non-small cell lung cancer (NSCLC).

METHODS

Patients with EGFR-mutant NSCLC who progressed as LMC after 3rd-generation tyrosine kinase inhibitors (EGFR-TKIs) were evaluated. A nanowire-based cfDNA assay was performed for genotyping cfDNA from the CSF and plasma. We focused on de novo EGFR C797S mutation and MET amplification, which are the most common mechanisms of resistance to 3rd-generation EGFR-TKIs.

RESULTS

Among 11 patients, five (45.5%) had progression only at the leptomeninges. The tumor-associated CSF-cfDNA was identified in eight (72.7%) patients, and plasma-cfDNA in six (54.5%) patients. In the CSF-cfDNA, EGFR C797S mutation and MET amplification were detected in four (36.3%) and two (18.2%) patients, respectively. Of four patients with the C797S-positive LMC, only one had concurrent CSF-T790M mutation. Three patients who had the C797S-positive LMC without CSF-T790M mutation, received 1st-2nd generation EGFR-TKIs and showed clinical benefits for 20.8, 17.8, and 8.8 weeks, respectively. Serial assessment with cfDNA in these patients demonstrated that the CSF levels of C797S mutation were decreased with radiological or neurological improvement but the plasma levels of T790M mutation were markedly increased before objective progression.

CONCLUSION

Genotyping CSF-cfDNA by the nanowire-based assay is feasible and effective in guiding the treatment of LMC in patients with EGFR-mutant NSCLC.

Magnetically driven microfluidics for isolation of circulating tumor cells

Circulating tumor cells (CTCs) largely contribute to cancer metastasis and show potential prognostic significance in cancer isolation and detection. Miniaturization has progressed significantly in the last decade which in turn enabled the development of several microfluidic systems. The microfluidic systems offer a controlled microenvironment for studies of fundamental cell biology, resulting in the rapid development of microfluidic isolation of CTCs. Due to the inherent ability of magnets to provide forces at a distance, the technology of CTCs isolation based on the magnetophoresis mechanism has become a routine methodology. This historical review aims to introduce two principles of magnetic isolation and recent techniques, facilitating research in this field and providing alternatives for researchers in their study of magnetic isolation. Researchers intend to promote effective CTC isolation and analysis as well as active development of next-generation cancer treatment. The first part of this review summarizes the primary principles based on positive and negative magnetophoretic isolation and describes the metrics for isolation performance. The second part presents a detailed overview of the factors that affect the performance of CTC magnetic isolation, including the magnetic field sources, functionalized magnetic nanoparticles, magnetic fluids, and magnetically driven microfluidic systems.

Refining Cancer Management Using Integrated Liquid Biopsy

Liquid biopsy has emerged in the last ten years as an appealing noninvasive strategy to support early cancer diagnosis and follow-up interventions. However, conventional liquid biopsy strategies involving specified biomarkers have encountered unexpected inconsistencies stemming from the use of different analytical methodologies. Recent reports have repeatedly demonstrated that integrated detection of multiple liquid biopsy biomarkers can significantly improve diagnostic performance by eliminating the influence of intratumoral heterogeneity. Herein, we review the progress in the field of liquid biopsy and propose a novel integrated liquid biopsy framework consisting of three categories: elementary, intermediate, and advanced integration. We also summarize the merits of the integration strategy and propose a roadmap toward refining cancer diagnosis, metastasis surveillance, and prognostication.

Projection method as a probe for multiplexing/demultiplexing of magnetically enriched biological tissues

The unmet demand for cheap, accurate, and fast multiplexing of biomarkers has urged nanobiotechnology to prioritize the invention of new biomarkers that make feasible the remote detection, identification, and quantification of biological units, such as regenerative tissues. Here, we introduce a novel approach that highlights magnetic nanowires (MNWs) with such capabilities. This method employs the stable magnetization states of MNWs as a unique characteristic that can be realized by projecting the MNWs' switching field on the backward field (P_Hb), also known as the irreversible switching field. Experimentally, several types of MNWs were directly synthesized inside polycarbonate tissues and their P_Hb characteristics were measured and analyzed. Our results show that the P_Hb gives an excellent identification and quantification characteristic for demultiplexing MNWs embedded in these tissues. Furthermore, this method significantly improves the characterization speed by a factor of 50×–100× that makes it superior to the current state of the art that ceased the progression of magnetic nanoparticles in multiplexing/demultiplexing applications.

Different polycarbonate tissues were enriched using magnetic nanowires with diverse magnetic signatures. Projection method successfully identifies and quantifies the complex combinations of the magnetically enriched polycarbonate tissues.

Modular Chamber Assembled with Cell-Replicated Surface for Capture of Cancer Cells

The capture of circulating tumor cells (CTCs) is mainly carried out with a small volume of blood using magnetic nanoparticles and complex microfluidics. In this study, we propose a CTC-capture apparatus based on a modular design and called this apparatus as the CTC chamber. Distinct from other CTC-capture apparatuses, the capacity of the CTC chamber could be altered by varying the number of CTC-capture modules to accommodate the different volumes of blood sample. The core component of the CTC-capture module was a polydimethylsiloxane (PDMS) film with cell-replicated topological structure and anti-EpCAM antibody coating. Both synergistic roles can enhance the capture yield of cancer cells. Furthermore, the CTC chamber was assembled with one or three CTC-capture modules for the capture of cancer cells from spiked blood samples representing late-stage (3 mL of blood, 10 cancer cells mL^-1) or middle-early stage (9 mL of blood, 1 cancer cell mL^-1) cancer. The results showed that high capture yield (EpCAM-positive, ∼80%; EpCAM-negative, ∼65%) and purity (EpCAM-positive, ∼90%; EpCAM-negative, ∼80%) could be obtained within 1 h. This economic and facile CTC chamber could therefore open up opportunities for designing the next-generation CTC detection devices suitable for the diagnosis of different stages of cancer.

Biomimetic human lung-on-a-chip for modeling disease investigation

The lung is the primary respiratory organ of the human body and has a complicated and precise tissue structure. It comprises conductive airways formed by the trachea, bronchi and bronchioles, and many alveoli, the smallest functional units where gas-exchange occurs via the unique gas-liquid exchange interface known as the respiratory membrane. In vitro bionic simulation of the lung or its microenvironment, therefore, presents a great challenge, which requires the joint efforts of anatomy, physics, material science, cell biology, tissue engineering, and other disciplines. With the development of micromachining and miniaturization technology, the concept of a microfluidics-based organ-on-a-chip has received great attention. An organ-on-a-chip is a small cell-culture device that can accurately simulate tissue and organ functions in vitro and has the potential to replace animal models in evaluations of drug toxicity and efficacy. A lung-on-a-chip, as one of the first proposed and developed organs-on-a-chip, provides new strategies for designing a bionic lung cell microenvironment and for in vitro construction of lung disease models, and it is expected to promote the development of basic research and translational medicine in drug evaluation, toxicological detection, and disease model-building for the lung. This review summarizes current lungs-on-a-chip models based on the lung-related cellular microenvironment, including the latest advances described in studies of lung injury, inflammation, lung cancer, and pulmonary fibrosis. This model should see effective use in clinical medicine to promote the development of precision medicine and individualized diagnosis and treatment.

[Progress of Liquid Biopsy in Early Diagnosis of Lung Cancer]

肺癌的早期诊断有利于提高患者的生存率。应用影像学方法对肺癌高风险人群进行筛查，可以起到早发现、早诊断的作用。越来越多的研究显示，液体活检（liquid biopsy）可以对该方法进行替代和补充。检测肺癌患者外周血中的循环肿瘤细胞（circulating tumor cells, CTCs）、循环肿瘤DNA（circulating tumor DNA, ctDNA）、微小核糖核酸（microRNA, miRNA）、外泌体（exosomes）、肿瘤血小板（tumor educated platelets, TEPs）可以用于肺癌的早期诊断，并且可能为影像学检查阴性的高风险人群提供相应的诊疗建议。全文就以上标志物的检测手段、在肺癌早期诊断中的价值以及存在优势与局限性进行综述，以期促进液体活检在肺癌早期诊断、与其他筛查手段相结合方面的应用。

Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies

Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.

Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges

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.