Multiplex digital PCR with digital melting curve analysis on a self-partitioning SlipChip

Microfluidic programmable strategies for channels and flow

This review summarizes programmable microfluidics, an advanced method for precise fluid control in microfluidic technology through microchannel design or liquid properties, referring to microvalves, micropumps, digital microfluidics, multiplexers, micromixers, slip-, and block-based configurations. Different microvalve types, including electrokinetic, hydraulic/pneumatic, pinch, phase-change and check valves, cater to diverse experimental needs. Programmable micropumps, such as passive and active micropumps, play a crucial role in achieving precise fluid control and automation. Due to their small size and high integration, microvalves and micropumps are widely used in medical devices and biological analysis. In addition, this review provides an in-depth exploration of the applications of digital microfluidics, multiplexed microfluidics, and mixer-based microfluidics in the manipulation of liquid movement, mixing, and splitting. These methodologies leverage the physical properties of liquids, such as capillary forces and dielectric forces, to achieve precise control over fluid dynamics. SlipChip technology, which branches into rotational SlipChip and translational SlipChip, controls fluid through sliding motion of the microchannel. On the other hand, innovative designs in microfluidic systems pursue better modularity, reconfigurability and ease of assembly. Different assembly strategies, from one-dimensional assembly blocks and two-dimensional Lego®-style blocks to three-dimensional reconfigurable modules, aim to enhance flexibility and accessibility. These technologies enhance user-friendliness and accessibility by offering integrated control systems, making them potentially usable outside of specialized technical labs. Microfluidic programmable strategies for channels and flow hold promising applications in biomedical research, chemical analysis and drug screening, providing theoretical and practical guidance for broader utilization in scientific research and practical applications.

All-In-One OsciDrop Digital PCR System for Automated and Highly Multiplexed Molecular Diagnostics

Digital PCR (dPCR) holds immense potential for precisely detecting nucleic acid markers essential for personalized medicine. However, its broader application is hindered by high consumable costs, complex procedures, and restricted multiplexing capabilities. To address these challenges, an all-in-one dPCR system is introduced that eliminates the need for microfabricated chips, offering fully automated operations and enhanced multiplexing capabilities. Using this innovative oscillation-induced droplet generation technique, OsciDrop, this system supports a comprehensive dPCR workflow, including precise liquid handling, pipette-based droplet printing, in situ thermocycling, multicolor fluorescence imaging, and machine learning-driven analysis. The system's reliability is demonstrated by quantifying reference materials and evaluating HER2 copy number variation in breast cancer. Its multiplexing capability is showcased with a quadruplex dPCR assay that detects key EGFR mutations, including 19Del, L858R, and T790M in lung cancer. Moreover, the digital stepwise melting analysis (dSMA) technique is introduced, enabling high-multiplex profiling of seven major EGFR variants spanning 35 subtypes. This innovative dPCR system presents a cost-effective and versatile alternative, overcoming existing limitations and paving the way for transformative advances in precision diagnostics.

Experimental investigation of confinement effect in single molecule amplification via real-time digital PCR on a multivolume droplet array SlipChip

BACKGROUND

Digital polymerase chain reaction (digital PCR) is an important quantitative nucleic acid analysis method in both life science research and clinical diagnostics. One important hypothesis is that by physically constraining a single nucleic acid molecule in a small volume, the relative concentration can be increased therefore further improving the analysis performance, and this is commonly defined as the confinement effect in digital PCR. However, experimental investigation of this confinement effect can be challenging since it requires a microfluidic device that can generate partitions of different volumes and an instrument that can monitor the kinetics of amplification. (96).

RESULTS

Here, we developed a real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip) that can generate droplet of 125 nL, 25 nL, 5 nL, and 1 nL by a simple "load-slip" operation. In the digital region, by reducing the volume, the relative concentration is increased, the amplification kinetic can be accelerated, and the time to reach the fluorescence threshold, or Cq value, can be reduced. When the copy number per well is much higher than one, the relative concentration is independent of the partition volume, thus the amplification kinetics are similar in different volume partitions. This system is not limited to studying the kinetics of digital nucleic acid amplification, it can also extend the dynamic range of the digital nucleic acid analysis by additional three orders of magnitude by combining a digital and an analog quantification algorithm. (140).

SIGNIFICANCE

In this study, we experimentally investigated for the first time the confinement effect in the community of digital PCR via a new real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip). And a wider dynamic range of quantification methods compared to conventional digital PCR was validated by this system. This system provides emerging opportunities for life science research and clinical diagnostics. (63).

Developing centrifugal force real-time digital PCR for detecting extremely low DNA concentration

Digital PCR (dPCR) is a technique for absolute quantification of nucleic acid molecules. To develop a dPCR technique that enables more accurate nucleic acid detection and quantification, we established a novel dPCR apparatus known as centrifugal force real-time dPCR (crdPCR). This system is efficient than other systems with only 2.14% liquid loss by dispensing samples using centrifugal force. Moreover, we applied a technique for analyzing the real-time graph of the each micro-wells and distinguishing true/false positives using artificial intelligence to mitigate the rain, a persistent issue with dPCR. The limits of detection and quantification were 1.38 and 4.19 copies/μL, respectively, showing a two-fold higher sensitivity than that of other comparable devices. With the integration of this new technology, crdPCR will significantly contribute to research on next-generation PCR targeting absolute micro-analysis.

Microfluidic systems for infectious disease diagnostics

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

Quantitative analysis of respiratory viruses based on lab-on-a-chip platform

The quantitative analysis of respiratory viruses is of great importance for rapid diagnosis, precision medicine, and prognosis. Several current quantitative analysis systems have been proposed and commercialized. Although they have been proven in trials, quantitative analyzes based on real samples are still complex, time-consuming, and expensive. Therefore, they are not able to directly quantify real samples. In this work, we presented a lab-on-a-chip platform combined with an automated control system to achieve quantitative analysis from samples to results. We developed a multilayer integrated chip to rapidly extract and quantify RNA of coronavirus disease 2019 (COVID-19) pseudovirus from large-volume nasal swab samples. The dependence of the magnetic bead size and the interfacial effect was studied for the first time, and the conditions of immiscible filtration assisted by surface tension (IFAST) method for nucleic acid extraction were optimized to increase the nucleic acid recovery rate up to 85%. Inside the chip, a pneumatic valve was developed for automatic opening and closing of the liquid channel. The integrated chip platform and automatic control system presented here are advantageous for use in resource-limited settings (RLS). In addition, our method can be extended to other respiratory viruses and other sample types.

Quantitative Investigation of Methylation Heterogeneity by Digital Melting Curve Analysis on a SlipChip for Atrial Fibrillation

Methylation is an essential epigenetic modification involved in regulating gene expression and maintaining genome stability. Methylation patterns can be heterogeneous, exhibiting variations in both level and density. However, current methods of methylation analysis, including sequencing, methylation-specific PCR, and high-resolution melting curve analysis (HRM), face limitations of high cost, time-consuming workflows, and the difficulty of both accurate heterogeneity analysis and precise quantification. Here, a droplet array SlipChip-based (da-SlipChip-based) digital melting curve analysis (MCA) method was developed for the accurate quantification of both methylation level (ratio of methylated molecules to total molecules) and methylation density (ratio of methylated CpG sites to total CpG sites). The SlipChip-based digital MCA system supplements an in situ thermal cycler with a fluorescence imaging module for real-time MCA. The da-SlipChip can generate 10,656 droplets of 1 nL each, which can be separated into four lanes, enabling the simultaneous analysis of four samples. This method's clinical application was demonstrated by analyzing samples from ten healthy individuals and twenty patients with atrial fibrillation (AF), the most common arrhythmia. This method can distinguish healthy individuals from those with AF of both the paroxysmal and persistent types. It also holds potential for broader application in various research and clinical settings requiring methylation analysis.

Smart-Plexer: a breakthrough workflow for hybrid development of multiplex PCR assays

Developing multiplex PCR assays requires extensive experimental testing, the number of which exponentially increases by the number of multiplexed targets. Dedicated efforts must be devoted to the design of optimal multiplex assays ensuring specific and sensitive identification of multiple analytes in a single well reaction. Inspired by data-driven approaches, we reinvent the process of developing and designing multiplex assays using a hybrid, simple workflow, named Smart-Plexer, which couples empirical testing of singleplex assays and computer simulation to develop optimised multiplex combinations. The Smart-Plexer analyses kinetic inter-target distances between amplification curves to generate optimal multiplex PCR primer sets for accurate multi-pathogen identification. In this study, the Smart-Plexer method is applied and evaluated for seven respiratory infection target detection using an optimised multiplexed PCR assay. Single-channel multiplex assays, together with the recently published data-driven methodology, Amplification Curve Analysis (ACA), were demonstrated to be capable of classifying the presence of desired targets in a single test for seven common respiratory infection pathogens.

Multiplex single-cell droplet PCR with machine learning for detection of high-risk human papillomaviruses

High-risk human papillomavirus (HPV) testing can significantly decline the incidence and mortality of cervical cancer. Microfluidic technology provides an effective method for accurate detection of high-risk HPV by utilizing multiplex single-cell droplet polymerase chain reaction (PCR). However, current strategies are limited by low-integration microfluidic chip, complex reagent system, expensive detection equipment and time-consuming droplet identification. Here, we developed a novel multiplex droplet PCR method that directly detected high-risk HPV sequences in single cells. A multiplex microfluidic chip integrating four flow-focusing structures was designed for one-step and parallel droplet preparation. Using single-cell droplet PCR, multi-target sequences were detected simultaneously based on a monochromatic fluorescence signal. We applied machine learning to automatically identify the large populations of single-cell droplets with 97% accuracy. HPV16, 18 and 45 sequences were sensitively detected without cross-contamination in mixed CaSki and Hela cells. The approach enables rapid and reliable detection of multi-target sequences in single cells, making it powerful for investigating cellular heterogeneity related to cancer diagnosis and treatment.

Advances in droplet digital polymerase chain reaction on microfluidic chips

The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.

Droplet Encoding-Pairing Enabled Multiplexed Digital Loop-Mediated Isothermal Amplification for Simultaneous Quantitative Detection of Multiple Pathogens

Despite the advantages of digital nucleic acid analysis (DNAA) in terms of sensitivity, precision, and resolution, current DNAA methods commonly suffer a limitation in multiplexing capacity. To address this issue, a droplet encoding-pairing enabled DNAA multiplexing strategy is developed, wherein unique tricolor combinations are deployed to index individual primer droplets. The template droplets and primer droplets are sequentially introduced into a microfluidic chip with a calabash-shaped microwell array and are pairwise trapped and merged in the microwells. Pre-merging and post-amplification image analysis with a machine learning algorithm is used to identify, enumerate, and address the droplets. By incorporating the amplification signals with droplet encoding information, simultaneous quantitative detection of multiple targets is achieved. This strategy allows for the establishment of flexible multiplexed DNAA by simply adjusting the primer droplet library. Its flexibility is demonstrated by establishing two multiplexed (8-plex) droplet digital loop-mediated isothermal amplification (mddLAMP) assays for individually detecting lower respiratory tract infection and urinary tract infection causative pathogens. Clinical sample analysis shows that the microbial detection outcomes of the mddLAMP assays are consistent with those of the conventional assay. This DNAA multiplexing strategy can achieve flexible high-order multiplexing on demand, making it a desirable tool for high-content pathogen detection.

Multiplex Digital Polymerase Chain Reaction on a Droplet Array SlipChip for Analysis of KRAS Mutations in Pancreatic Cancer

Pancreatic cancer is a terminal disease with high mortality and very poor prognosis. A sensitive and quantitative analysis of KRAS mutations in pancreatic cancer provides a tool not only to understand the biological mechanisms of pancreatic cancer but also for diagnosis and treatment monitoring. Digital polymerase chain reaction (PCR) is a promising tool for KRAS mutation analysis, but current methods generally require a complex microfluidic handling system, which can be challenging to implement in routine research and point-of-care clinical diagnostics. Here, we present a droplet-array SlipChip (da-SlipChip) for the multiplex quantification of KRAS G12D, V, R, and C mutant genes with the wild-type (WT) gene background by dual color (FAM/ROX) fluorescence detection. This da-SlipChip is a high-density microwell array of 21,696 wells of 200 pL in 4 by 5424 microwell format with simple loading and slipping operation. It does not require the same precise alignment of microfeatures on the different plates that are acquired by the traditional digital PCR SlipChip. This device can provide accurate quantification of both mutant genes and the WT KRAS gene. We collected tumor tissue, paired normal pancreatic tissue, and other normal tissues from 18 pancreatic cancer patients and analyzed the mutation profiles of KRAS G12D, V, R, and C in these samples; the results from the multiplex digital PCR on da-SlipChip agree well with those of next-generation sequencing (NGS). This da-SlipChip moves digital PCR closer to the practical point-of-care applications not only for detecting KRAS mutations in pancreatic cancer but also for other applications that require precise nucleic acid quantification with high sensitivity.

Parallel multistep digital analysis SlipChip demonstrated with the quantification of nucleic acid by digital LAMP-CRISPR

Digital biological analysis compartmentalizes targets of interest, such as nucleic acids, proteins, and cells, to a single event level and performs detection and further investigation. Microfluidic-based digital biological analysis methods, including digital PCR, digital protein analysis, and digital cell analysis, have demonstrated superior advantages in research applications and clinical diagnostics. However, most of the methods are still based on a one-step "divide and detect" strategy, and it is challenging for these methods to perform further parallel manipulation of reaction partitions to achieve "divide, manipulate, and analyze" capabilities. Here, we present a parallel multistep digital analysis (PAMDA) SlipChip for the parallel multistep manipulation of a large number of droplets for digital biological analysis, demonstrated by the quantification of SARS-CoV-2 nucleic acids by a two-step digital isothermal amplification combined with clustered regularly interspaced short palindromic repeats (CRISPR). This PAMDA SlipChip utilizes a "chain-of-pearl" channel with a self-partitioning droplet formation mechanism that does not require the precise alignment of microfeatures for fluidic loading as the traditional SlipChip design. This device can first generate 2400 3.2 nanoliter droplets to perform digital loop-mediated isothermal amplification (LAMP) and then deliver reagents containing Cas12a protein and crRNA to each individual partition in parallel to simultaneously initiate digital CRISPR detection by a simple multistep slipping operation. This PAMDA SlipChip not only provides a promising tool to perform digital CRISPR with a flexible assay and workflow design but can also be applied for a broad range of applications in digital biological analysis that require multistep manipulation of partitions in parallel.

A Specific and Sensitive Aptamer-Based Digital PCR Chip for Salmonella typhimurium Detection

Food poisoning and infectious diseases caused by Salmonella typhimurium (S. typhimurium) are serious public health concerns for human health and food safety. The diversity and complexity of food matrices pose great challenges for rapid and ultra-sensitive detection of S. typhimurium in food samples. A method capable of identification, detection, and quantification of S. typhimurium is essential for addressing these issues. In this study, aptamer-coated magnetic beads (Apt-MBs) are employed as capture bio-probes to specifically and selectively concentrate S. typhimurium in food samples. A self-priming chip-based digital PCR was then presented as another biosensor for on-site detection and quantification of S. typhimurium cells. The chip we developed was robust and did not require any external power for sample loading. The combination of Apt-MBs with an on-chip digital detection realized the integration into lab-on-a-chip-based biosensors for on-site monitoring of foodborne pathogens. It was possible to capture and detect S. typhimurium cells as low as 90 CFU/reaction with a capture efficiency of 94.5%. Additionally, the whole process only took about 2 h. This unique platform could also be used to monitor other target bacteria with high specificity and sensitivity by utilizing different aptamers. Furthermore, the platform has potential applications in point-of-care testing in the future.

Single-channel digital LAMP multiplexing using amplification curve analysis

We demonstrate LAMP multiplexing (5-plex) in a single reaction with a single fluorescent channel using the machine learning-based method amplification curve analysis, showing a classification accuracy of 91.33% for detection of respiratory pathogens.