Automated screening using microfluidic chip-based PCR and product detection to assess risk of BK virus-associated nephropathy in renal transplant recipients

Magnetic-based Microfluidic Chip: A Powerful Tool for Pathogen Detection and Affinity Reagents Selection

The global outbreak of pathogen diseases has brought a huge risk to human lives and social development. Rapid diagnosis is the key strategy to fight against pathogen diseases. Development of detection methods and discovery of related affinity reagents are important parts of pathogen diagnosis. Conventional detection methods and affinity reagents discovery have some problems including much reagent consumption and labor intensity. Magnetic-based microfluidic chip integrates the unique advantages of magnetism and microfluidic technology, improving a powerful tool for pathogen detection and their affinity reagent discovery. This review provides a summary about the summary of pathogen detection through magnetic-based microfluidic chip, which refers to the pathogen nucleic acid detection (including extraction, amplification and signal acquisition), pathogen proteins and antibodies detection. Meanwhile, affinity reagents are served as the critical tool to specially capture pathogens. New affinity reagents are discovered to further facilitate the pathogen diagnosis. Microfluidic technology has also emerged as a powerful tool for affinity reagents discovery. Thus, this review further introduced the selection progress of aptamer as next generation affinity through the magnetic-based microfluidic technology. Using this selection technology shows great potential to improve selection performance, including integration and highly efficient selection. Finally, an outlook is given on how this field will develop on the basis of ongoing pathogen challenges.

A Comparison of Optical, Electrochemical, Magnetic, and Colorimetric Point-of-Care Biosensors for Infectious Disease Diagnosis

Each year, infectious diseases are responsible for millions of deaths, most of which occur in the rural areas of developing countries. Many of the infectious disease diagnostic tools used today require a great deal of time, a laboratory setting, and trained personnel. Due to this, the need for effective point-of-care (POC) diagnostic tools is greatly increasing with an emphasis on affordability, portability, sensitivity, specificity, timeliness, and ease of use. In this Review, we discuss the various diagnostic modalities that have been utilized toward this end and are being further developed to create POC diagnostic technologies, and we focus on potential effectiveness in resource-limited settings. The main modalities discussed herein are optical-, electrochemical-, magnetic-, and colorimetric-based modalities utilized in diagnostic technologies for infectious diseases. Each of these modalities feature pros and cons when considering application in POC settings but, overall, reveal a promising outlook for the future of this field of technological development.

Applications of Microfluidic Devices for Urology

Microfluidics is considered an important technology that is suitable for numerous biomedical applications, including cancer diagnosis, metastasis, drug delivery, and tissue engineering. Although microfluidics is still considered to be a new approach in urological research, several pioneering studies have been reported in recent years. In this paper, we reviewed urological research works using microfluidic devices. Microfluidic devices were used for the detection of prostate and bladder cancer and the characterization of cancer microenvironments. The potential applications of microfluidics in urinary analysis and sperm sorting were demonstrated. The use of microfluidic devices in urology research can provide high-throughput, high-precision, and low-cost analyzing platforms.

Current Technologies and Recent Developments for Screening of HPV-Associated Cervical and Oropharyngeal Cancers

Mucosal infection by the human papillomavirus (HPV) is responsible for a growing number of malignancies, predominantly represented by cervical cancer and oropharyngeal squamous cell carcinoma. Because of the prevalence of the virus, persistence of infection, and long latency period, novel and low-cost methods are needed for effective population level screening and monitoring. We review established methods for screening of cervical and oral cancer as well as commercially-available techniques for detection of HPV DNA. We then describe the ongoing development of microfluidic nucleic acid-based biosensors to evaluate circulating host microRNAs that are produced in response to an oncogenic HPV infection. The goal is to develop an ideal screening platform that is low-cost, portable, and easy to use, with appropriate signal stability, sensitivity and specificity. Advances in technologies for sample lysis, pre-treatment and concentration, and multiplexed nucleic acid detection are provided. Continued development of these devices provides opportunities for cancer screening in low resource settings, for point-of-care diagnostics and self-screening, and for monitoring response to vaccination or surgical treatment.

Sample introduction interface for on-chip nucleic acid-based analysis of Helicobacter pylori from stool samples

Despite recent advances in microfluidic-based integrated diagnostic systems, the sample introduction interface, especially with regards to large volume samples, has often been neglected. We present a sample introduction interface that allows direct on-chip processing of crude stool samples for the detection of Helicobacter pylori (H. pylori). The principle of IFAST (immiscible filtration assisted by surface tension) was adapted to include a large volume sample chamber with a septum-based interface for stool sample introduction. Solid chaotropic salt and dry superparamagnetic particles (PMPs) could be stored on-chip and reconstituted upon sample addition, simplifying the process of release of DNA from H. pylori cells and its binding to the PMPs. Finally, the PMPs were pulled via a magnet through a washing chamber containing an immiscible oil solution and into an elution chamber where the DNA was released into aqueous media for subsequent analysis. The entire process required only 7 min while enabling a 40-fold reduction in working volume from crude biological samples. The combination of a real-world interface and rapid DNA extraction offers the potential for the methodology to be used in point-of-care (POC) devices.

Integrated, DC voltage-driven nucleic acid diagnostic platform for real sample analysis: Detection of oral cancer

We present an integrated and low-cost microfluidic platform capable of extraction of nucleic acids from real biological samples. We demonstrate the application of this platform in pathogen detection and cancer screening. The integrated platform consists of three units including a pretreatment unit for separation of nucleic acids from lysates, a preconcentration unit for concentration of isolated nucleic acids and a sensing unit localized at a designated position on the chip for specific detection of the target nucleic acid. The platform is based on various electrokinetic phenomena exhibited by ion exchange membranes in a DC electrical field that allow them to serve as molecular filters, analyte preconcentrators and sensors. In this manuscript, we describe each unit of the integrated chip separately and show specific detection of a microRNA (miRNA 146a) biomarker associated with oral cancer as a proof-of-concept experiment. This platform technology can easily be extended to other targets of interest by optimizing the properties of the ion exchange membranes and the specific probes functionalized onto the sensors.

Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE): epidemiology, emerging organisms, and economics

Background

Each year in Canada there are 5 million episodes of acute gastroenteritis (AGE) with up to 70 % attributed to an unidentified pathogen. Moreover, 90 % of individuals with AGE do not seek care when ill, thus, burden of disease estimates are limited by under-diagnosing and under-reporting. Further, little is known about the pathogens causing AGE as the majority of episodes are attributed to an “unidentified” etiology. Our team has two main objectives: 1) to improve health through enhanced enteric pathogen identification; 2) to develop economic models incorporating pathogen burden and societal preferences to inform enteric vaccine decision making.

Methods/Design

This project involves multiple stages: 1) Molecular microbiology experts will participate in a modified Delphi process designed to define criteria to aid in interpreting positive molecular enteric pathogen test results. 2) Clinical data and specimens will be collected from children aged 0–18 years, with vomiting and/or diarrhea who seek medical care in emergency departments, primary care clinics and from those who contact a provincial medical advice line but who do not seek care. Samples to be collected will include stool, rectal swabs (N = 2), and an oral swab. Specimens will be tested employing 1) stool culture; 2) in-house multiplex (N = 5) viral polymerase chain reaction (PCR) panel; and 3) multi-target (N = 15) PCR commercially available array. All participants will have follow-up data collected 14 days later to enable calculation of a Modified Vesikari Scale score and a Burden of Disease Index. Specimens will also be collected from asymptomatic children during their well child vaccination visits to a provincial public health clinic. Following the completion of the initial phases, discrete choice experiments will be conducted to enable a better understanding of societal preferences for diagnostic testing and vaccine policy. All of the results obtained will be integrated into economic models.

Discussion

This study is collecting novel samples (e.g., oral swabs) from previously untested groups of children (e.g., those not seeking medical care) which are then undergoing extensive molecular testing to shed a new perspective on the epidemiology of AGE. The knowledge gained will provide the broadest understanding of the epidemiology of vomiting and diarrhea of children to date.

Microfluidic platform towards point-of-care diagnostics in infectious diseases

Rapid and timely diagnosis of infectious diseases is a critical determinant of clinical outcomes and general public health. For the detection of various pathogens, microfluidics-based platforms offer many advantages, including speed, cost, portability, high throughput, and automation. This review provides an overview of the recent advances in microfluidic technologies for point-of-care (POC) diagnostics for infectious diseases. The key aspects of such technologies for the development of a fully integrated POC platform are introduced, including sample preparation, on-chip nucleic acid analysis and immunoassay, and system integration/automation. The current challenges to practical implementation of this technology are discussed together with future perspectives.

Magnetic barcode assay for genetic detection of pathogens

The task of rapidly identifying patients infected with Mycobacterium tuberculosis in resource-constrained environments remains a challenge. A sensitive and robust platform that does not require bacterial isolation or culture is critical in making informed diagnostic and therapeutic decisions. Here we introduce a platform for the detection of nucleic acids based on a magnetic barcoding strategy. PCR-amplified mycobacterial genes are sequence-specifically captured on microspheres, labelled by magnetic nanoprobes and detected by nuclear magnetic resonance. All components are integrated into a single, small fluidic cartridge for streamlined on-chip operation. We use this platform to detect M. tuberculosis and identify drug-resistance strains from mechanically processed sputum samples within 2.5 h. The specificity of the assay is confirmed by detecting a panel of clinically relevant non-M. tuberculosis bacteria, and the clinical utility is demonstrated by the measurements in M. tuberculosis-positive patient specimens. Combined with portable systems, the magnetic barcode assay holds promise to become a sensitive, high-throughput and low-cost platform for point-of-care diagnostics.

Nucleic acid amplification using microfluidic systems

In the post-human-genome-project era, the development of molecular diagnostic techniques has advanced the frontiers of biomedical research. Nucleic-acid-based technology (NAT) plays an especially important role in molecular diagnosis. However, most research and clinical protocols still rely on the manual analysis of individual samples by skilled technicians which is a time-consuming and labor-intensive process. Recently, with advances in microfluidic designs, integrated micro total-analysis-systems have emerged to overcome the limitations of traditional detection assays. These microfluidic systems have the capability to rapidly perform experiments in parallel and with a high-throughput which allows a NAT analysis to be completed in a few hours or even a few minutes. These features have a significant beneficial influence on many aspects of traditional biological or biochemical research and this new technology is promising for improving molecular diagnosis. Thus, in the foreseeable future, microfluidic systems developed for molecular diagnosis using NAT will become an important tool in clinical diagnosis. One of the critical issues for NAT is nucleic acid amplification. In this review article, recent advances in nucleic acid amplification techniques using microfluidic systems will be reviewed. Different approaches for fast amplification of nucleic acids for molecular diagnosis will be highlighted.

Real-time quantitative PCR, pathogen detection and MIQE

Nucleic acids are the ultimate biomarker and real-time PCR (qPCR) is firmly established as the method of choice for nucleic acid detection. Together, they allow the accurate, sensitive and specific identification of pathogens, and the use of qPCR has become routine in diagnostic laboratories. The reliability of qPCR-based assays relies on a combination of optimal sample selection, assay design and validation as well as appropriate data analysis and the "Minimal Information for the Publication of real-time PCR" (MIQE) guidelines aim to improve both the reliability of assay design as well as the transparency of reporting, essential conditions if qPCR is to remain the benchmark technology for molecular diagnosis.

Advances in microfluidic PCR for point-of-care infectious disease diagnostics

Global burdens from existing or emerging infectious diseases emphasize the need for point-of-care (POC) diagnostics to enhance timely recognition and intervention. Molecular approaches based on PCR methods have made significant inroads by improving detection time and accuracy but are still largely hampered by resource-intensive processing in centralized laboratories, thereby precluding their routine bedside- or field-use. Microfluidic technologies have enabled miniaturization of PCR processes onto a chip device with potential benefits including speed, cost, portability, throughput, and automation. In this review, we provide an overview of recent advances in microfluidic PCR technologies and discuss practical issues and perspectives related to implementing them into infectious disease diagnostics.

Genetic analysis of H1N1 influenza virus from throat swab samples in a microfluidic system for point-of-care diagnostics

The ability to obtain sequence-specific genetic information about rare target organisms directly from complex biological samples at the point-of-care would transform many areas of biotechnology. Microfluidics technology offers compelling tools for integrating multiple biochemical processes in a single device, but despite significant progress, only limited examples have shown specific, genetic analysis of clinical samples within the context of a fully integrated, portable platform. Herein we present the Magnetic Integrated Microfluidic Electrochemical Detector (MIMED) that integrates sample preparation and electrochemical sensors in a monolithic disposable device to detect RNA-based virus directly from throat swab samples. By combining immunomagnetic target capture, concentration, and purification, reverse-transcriptase polymerase chain reaction (RT-PCR) and single-stranded DNA (ssDNA) generation in the sample preparation chamber, as well as sequence-specific electrochemical DNA detection in the electrochemical cell, we demonstrate the detection of influenza H1N1 in throat swab samples at loads as low as 10 TCID(50), 4 orders of magnitude below the clinical titer for this virus. Given the availability of affinity reagents for a broad range of pathogens, our system offers a general approach for multitarget diagnostics at the point-of-care.

Urine analysis in microfluidic devices

Microfluidics has attracted considerable attention since its early development in the 1980s and has experienced rapid growth in the past three decades due to advantages associated with miniaturization, integration and automation. Urine analysis is a common, fast and inexpensive clinical diagnostic tool in health care. In this article, we will be reviewing recent works starting from 2005 to the present for urine analysis using microfluidic devices or systems and to provide in-depth commentary about these techniques. Moreover, commercial strips that are often treated as chips and their readers for urine analysis will also be briefly discussed. We start with an introduction to the physiological significance of various components or measurement standards in urine analysis, followed by a brief introduction to enabling microfluidic technologies. Then, microfluidic devices or systems for sample pretreatments and for sensing urinary macromolecules, micromolecules, as well as multiplexed analysis are reviewed, in this sequence. Moreover, a microfluidic chip for urinary proteome profiling is also discussed, followed by a section discussing commercial products. Finally, the authors' perspectives on microfluidic-based urine analysis are provided. These advancements in microfluidic techniques for urine analysis may improve current routine clinical practices, particularly for point-of-care (POC) applications.

Microfabrication and applications of opto-microfluidic sensors

A review of research activities on opto-microfluidic sensors carried out by the research groups in Canada is presented. After a brief introduction of this exciting research field, detailed discussion is focused on different techniques for the fabrication of opto-microfluidic sensors, and various applications of these devices for bioanalysis, chemical detection, and optical measurement. Our current research on femtosecond laser microfabrication of optofluidic devices is introduced and some experimental results are elaborated. The research on opto-microfluidics provides highly sensitive opto-microfluidic sensors for practical applications with significant advantages of portability, efficiency, sensitivity, versatility, and low cost.

In-gel technology for PCR genotyping and pathogen detection

This work describes the use of polyacrylamide gel and PCR reagents photopolymerized in a mold to create an array of semisolid posts that serve as reaction vessels for parallel PCR amplification of an externally added template. DNA amplification occurred in a cylindrical, self-standing 9 × 9 array of gel posts each less than 1 μL in volume. Photopolymerization of the gel with an intercalating dye added prior to polymerization permitted acquisition of real-time PCR data and melting curve analysis data without the need for any type of post-PCR staining procedures. PCR was equally efficient and reproducible when template DNA was polymerized within the gel or when exogenous template was added atop precast gel posts. PCR amplification occurred with template from purified DNA or from raw urine of patients with BK viruria. Multiple primer sets can be utilized per gel post array with no detectable cross contamination. As few as 34 BK virus templates were consistently detected by PCR in an individual gel post. Amplification of HPA1 and FGFR2 genes in human genomic DNA (gDNA) required as little as 2-5 ng of gDNA template/gel post. The device prototype includes a Peltier element for PCR thermal cycling and a CCD camera to capture fluorescence for product detection. Our technology is amenable to integration in point of care microdevices.

Integrated capillary electrophoresis microsystem for multiplex analysis of human respiratory viruses

We developed a two-layer, four-channel polymerase chain reaction (PCR)-capillary electrophoresis microdevice that integrates nucleic acid amplification, sample cleanup and concentration, capillary electrophoretic separation, and detection for multiplex analysis of four human respiratory viral pathogens, influenza A, influenza B, coronavirus OC43, and human metapneumovirus. Biotinylated and fluorescently labeled double-stranded (ds) deoxyribonucleic acid (DNA) amplification products are generated in a 100 nL PCR reactor incorporating an integrated heater and a temperature sensor. After amplification, the products are captured and concentrated in a cross-linked acrylamide gel capture matrix copolymerized with acrydite-functionalized streptavidin-capture agents. Thermal dehybridization releases the fluorescently labeled DNA strand for capillary electrophoresis injection, separation, and detection. Using plasmid standards containing the viral genes of interest, each target can be detected starting from as few as 10 copies/reactor. When a two-step reverse transcription PCR amplification is employed, the device can detect ribonucleic acid (RNA) analogues of all four viral targets with detection limits in the range of 25-100 copies/reactor. The utility of the microdevice for analyzing samples from nasopharyngeal swabs is demonstrated. When size-based separation is combined with four-color detection, this platform provides excellent product discrimination, making it readily extendable to higher-order multiplex assays. This portable microsystem is also suitable for performing automated assays in point-of-care diagnostic applications.

Development of a microfluidic chip-based plasmid miniprep

Plasmids are the workhorse of contemporary molecular biology, serving as vectors in the multitude of molecular cloning approaches now available. Plasmid minipreps are a routine and essential means of extracting plasmid DNA from bacteria, such as Escherichia coli, for identification, characterization, and further manipulation. Although there have been many approaches described and miniprep kits are commercially available, traditional minipreps typically require more than 16h, including the time needed for bacterial cell culture. Here we describe the development of a microfluidic chip (MFC)-based miniprep that uses on-chip lysis and trapping of large DNA in agarose to differentially separate plasmid DNA from the bacterial chromosome. Our approach greatly decreases both the time required for the miniprep itself and the time required for growth of the bacterial cultures because our on-chip miniprep uses 10(5) times fewer E. coli cells. Because the quality of the isolated plasmid is comparable to that obtained using conventional miniprep protocols, this approach allows growth of E. coli and isolation of plasmid within hours, thereby making it ideal for rapid screening approaches. This MFC-based miniprep, coupled with recently demonstrated on-chip transfection capabilities, lays the groundwork for seamless manipulation of plasmids on MFC platforms.

Simply and reliably integrating micro heaters/sensors in a monolithic PCR-CE microfluidic genetic analysis system

A novel fabrication process was presented to construct a monolithic integrated PCR-CE microfluidic DNA analysis system as a step toward building a total genetic analysis microsystem. Microfabricated Titanium/Platinum (Ti/Pt) heaters and resistance temperature detectors (RTDs) were integrated on the backside of a bonded glass chip to provide good thermal transfer and precise temperature detection for the drilled PCR-wells. This heater/RTD integration procedure was simple and reliable, and the resulting metal layer can be easily renewed when the Ti/Pt layer was damaged in later use or novel heater/RTD design was desired. A straightforward "RTD-calibration" method was employed to optimize the chip-based thermal cycling conditions. This method was convenient and rapid, comparing with a conventional RTD-calibration/temperature adjustment method. The highest ramping rates of 14 degrees C/s for heating and 5 degrees C/s for cooling in a 3-microL reaction volume allow 30 complete PCR cycles in about 33 min. After effectively passivating the PCR-well surface, successful lambda-phage DNA amplifications were achieved using a two- or three-temperature cycling protocol. The functionality and performance of the integrated microsystem were demonstrated by successful amplification and subsequent on-line separation/sizing of lambda-phage DNA. A rapid assay for Hepatitis B virus, one of the major human pathogens, was performed in less than 45 min, demonstrating that the developed PCR-CE microsystem was capable of performing automatic and high-speed genetic analysis.

Integrated capture, concentration, polymerase chain reaction, and capillary electrophoretic analysis of pathogens on a chip

A laboratory-on-a-chip system for pathogen detection is presented that integrates cell preconcentration, purification, polymerase chain reaction (PCR), and capillary electrophoretic (CE) analysis. The microdevice is composed of micropumps and valves, a cell capture structure, a 100 nL PCR reactor, and a 5 cm long CE column for amplicon separation. Sample volumes ranging from 10 to 100 microL are introduced and driven through a fluidized bed of magnetically constrained immunomagnetic beads where the target cells are captured. After cell capture, beads are transferred using the on-chip pumps to the PCR reactor for DNA amplification. The resulting PCR products are electrophoretically injected onto the CE column for separation and detection of Escherichia coli K12 and E. coli O157 targets. A detection limit of 0.2 cfu/microL is achieved using the E. coli O157 target and an input volume of 50 microL. Finally, the sensitive detection of E. coli O157 in the presence of K12 at a ratio of 1:1000 illustrates the capability of our system to identify target cells in a high commensal background. This cell capture-PCR-CE microsystem is a significant advance in the development of rapid, sensitive, and specific laboratory-on-a-chip devices for pathogen detection.

Microfluidic systems for pathogen sensing: a review

Rapid pathogen sensing remains a pressing issue today since conventional identification methodsare tedious, cost intensive and time consuming, typically requiring from 48 to 72 h. In turn, chip based technologies, such as microarrays and microfluidic biochips, offer real alternatives capable of filling this technological gap. In particular microfluidic biochips make the development of fast, sensitive and portable diagnostic tools possible, thus promising rapid and accurate detection of a variety of pathogens. This paper will provide a broad overview of the novel achievements in the field of pathogen sensing by focusing on methods and devices that compliment microfluidics.

Multiplexed optical pathogen detection with lab-on-a-chip devices

Infectious diseases are still a main cause of human morbidity and mortality. Advanced diagnostics is considered to be a key driver to improve the respective therapeutic outcome. The main factors influencing the impact of diagnostics include: assay speed, availability, information content, in-vitro diagnostics and cost, for which molecular assays are providing the most promising opportunities. Miniaturisation and integration of assay steps into lab-on-a-chip devices has been described as an appropriate way to speed up assay time and make assays available onsite at competitive costs. As meaningful assays for infectious diseases need to include a whole range of clinical relevant information about the pathogen, multiplexed functionality is often required for which optical transduction is particularly well suited. The aim of this review is to assess existing developments in this field and to give an outlook on future requirements and solutions.

Strategies for enhancing the speed and integration of microchip genetic amplification

In this work, we explore the use of methods that allow a significant acceleration of genetic analysis within microchips fabricated from low thermal conductivity materials such as glass or polymers. Although these materials are highly suitable for integrating a number of genetic analysis techniques onto lab-on-a-chip devices, their low thermal conductivity limits the rate at which heat can be transferred and hence lowers the speed of thermal cycling. However, short thermal cycling times are the key to bringing PCR to clinical point-of-care applications. Although shrinking the PCR reaction chamber volume can increase the speed of thermal cycling, this strategy is not always suitable, particularly when dealing with clinical samples with low analyte concentrations. In the present work, we combine two alternate strategies for decreasing the time required to perform PCR: implementing a heat sink and optimizing the PCR protocol. First, the heat sink substantially reduces the thermal resistance opposing heat dissipation into the ambient environment, and eliminates the parasitic thermal capacitance of the regions in the microchip that do not require heating. The low thermal conductivity of glass is used to our advantage to design the heat-sink placement to achieve fast thermal transitions while maintaining low power consumption. Second, we explore the application of two-stage PCR to provide a further reduction in the time required to perform genetic amplification by merging the annealing and extension stages of the commonly used three-stage PCR approach. In combination, we reduce the time required to perform thermal cycling by roughly a factor of 3 while improving the temperature control.

Microchip capillary electrophoresis

Microchip capillary electrophoresis (MCE) is gaining popularity due to the developments of simple microfabrication methods under nonstringent laboratory conditions. Moreover, the low material and production costs of polymer-based microchips have further stimulated advances in the applications of MCE in various fields, including clinical analysis, drug screening, biomarker identification, and biosensing. In this chapter, a simple and robust protocol for fabrication of microchips for lab-on-chip testing and microchip electrophoresis is described. The microchips are hybrid poly(dimethylsiloxane) (PDMS)/glass microchips, which are produced by a combination of photolithography and micromolding processes. This type of microchip has been used in a wide range of analyses.

Sample preparation: the weak link in microfluidics-based biodetection

As a broad generalization, clinicians and laboratory personnel who use microfluidics-based automated or semi-automated instrumentation to perform biomedical assays on real-world samples are more pleased with the state of the assays than they are with the state of the front-end sample preparation. The end-to-end procedure requires one to collect, manipulate, prepare, and analyze the sample. The appeal of microfluidics for this procedure is partly based on its combination of small size and its ability to process very small liquid volumes, thus minimizing the use of possibly expensive reagents. However, real-world samples are often large and incompatible with the input port and the mum-scale channels of a microfluidic device, and very small liquid volumes can be inappropriate in analyzing low concentrations of target analytes. It can be a worthy challenge to take a raw sample, introduce it into a microfluidics-based system, and perform the sample preparation, which may include separation and concentration of the target analytes, so that one can benefit from the reagent-conserving small volumes and obtain the correct answer when finally implementing the assay of interest.

An integrated CMOS high voltage supply for lab-on-a-chip systems

Electrophoresis is a mainstay of lab-on-a-chip (LOC) implementations of molecular biology procedures and is the basis of many medical diagnostics. High voltage (HV) power supplies are necessary in electrophoresis instruments and are a significant part of the overall system cost. This cost of instrumentation is a significant impediment to making LOC technologies more widely available. We believe one approach to overcoming this problem is to use microelectronic technology (complementary metal-oxide semiconductor, CMOS) to generate and control the HV. We present a CMOS-based chip (3 mm x 2.9 mm) that generates high voltages (hundreds of volts), switches HV outputs, and is powered by a 5 V input supply (total power of 28 mW) while being controlled using a standard computer serial interface. Microchip electrophoresis with laser induced fluorescence (LIF) detection is implemented using this HV CMOS chip. With the other advancements made in the LOC community (e.g. micro-fluidic and optical devices), these CMOS chips may ultimately enable 'true' LOC solutions where essentially all the microfluidics, photonics and electronics are on a single chip.

Electrophoretic microfluidic devices for mutation detection in clinical diagnostics

BACKGROUND

In an era of growing interest in personalized medicine - where ubiquitous patient genotyping holds unprecedented clinical utility - rapid, sensitive and low-cost methodologies will be required for the detection of genetic variants correlative with disease. Electrophoretic microfluidic devices have emerged as a promising platform for such analyses, inherently offering faster analysis, excellent reagent economy, a small laboratory footprint and potentially seamless integration of multiple analytical steps.

OBJECTIVE

Although glass and polymeric microchips have recently been developed for a wide variety of medical applications, this review focuses on their application to the detection of clinically relevant genomic DNA mutations and polymorphisms.

METHOD

Mutation analysis techniques, including direct gene sizing, enzyme-based assays, heteroduplex analysis, single-strand conformational polymorphism analysis, and multiplex, allele-specific and methylation-specific PCR are included.

CONCLUSION

Further development of 'lab-on-a-chip' or 'micro total analysis system' technologies ultimately aims to streamline and miniaturize the entire genetic analysis process, enabling rapid, point-of-care analysis for molecular diagnostics.

Electrically controlled microvalves to integrate microchip polymerase chain reaction and capillary electrophoresis

Microvalves are key in realizing portable miniaturized diagnostic platforms. We present a scalable microvalve that integrates well with standard lab on a chip (LOC) implementations, yet which requires essentially no external infrastructure for its operation. This electrically controlled, phase-change microvalve is used to integrate genetic amplification and analysis via capillary electrophoresis--the basis of many diagnostics. The microvalve is actuated using a polymer (polyethylene glycol, PEG) that exhibits a large volumetric change between its solid and liquid phases. Both the phase change of the PEG and the genetic amplification via polymerase chain reaction (PCR) are thermally controlled using thin film resistive elements that are patterned using standard microfabrication methods. By contrast with many other valve technologies, these microvalves and their control interface scale down in size readily. The novelty here lies in the use of fully integrated microvalves that require only electrical connections to realize a portable and inexpensive genetic analysis platform.

A microfluidic study of mechanisms in the electrophoresis of supercoiled DNA

In this work, microfluidic chips were used to study the electrophoresis of supercoiled DNA (SC DNA) in agarose. This system allowed us to study the electrophoretic and trapping behaviours of SC DNA of various lengths, at various fields and separation distances. Near a critical electric field the DNA is trapped such that the concentration falls exponentially with distance. The trapping of such circular DNA has been explained in terms of the 'lobster trap' or 'impalement' model where shorter fibres become trapping sites at higher fields, leading to an ongoing (and gradual) increase in trapping with increasing field. By contrast, the present study suggests that under some circumstances the traps have a barrier such that only when the DNA has sufficient energy (at high enough fields) can it become trapped, leading to a sudden transition in behaviours at the critical field. We propose an 'activated impalement' mechanism of trapping in which only at sufficiently high fields is the SC DNA impaled and trapped for long times. The critical electric field appears to be inversely proportional to the length of the DNA molecule, suggesting that the force required to impale the SC DNA is constant.

Integrated wavelength-selective optical waveguides for microfluidic-based laser-induced fluorescence detection

We demonstrate the fabrication and characterization of a novel, inexpensive microchip capable of laser induced fluorescence (LIF) detection using integrated waveguides with built-in optical filters. Integrated wavelength-selective optical waveguides are fabricated by doping poly(dimethysiloxane) (PDMS) with dye molecules. Liquid-core waveguides are created within dye-doped PDMS microfluidic chips by filling channels with high refractive index liquids. Dye molecules are allowed to diffuse into the liquid core from the surrounding dye-doped PDMS. The amount of diffusion is controlled by choosing either polar (low diffusion) or apolar (high diffusion) liquid waveguide cores. The doping dye is chosen to absorb excitation light and to transmit fluorescence emitted by the sample under test. After 24 h, apolar waveguides demonstrate propagation losses of 120 dB cm(-1) (532 nm) and 4.4 dB cm(-1) (633 nm) while polar waveguides experience losses of 8.2 dB cm(-1) (532 nm) and 1.1 dB cm(-1) (633 nm) where 532 and 633 nm light represent the excitation and fluorescence wavelengths, respectively. We demonstrate the separation and detection of end-labelled DNA fragments using polar waveguides for excitation light delivery and apolar waveguides for fluorescence collection. We demonstrate that the dye-doped waveguides can provide performance comparable to a commercial dielectric filter; however, for the present choice of dye, their ultimate performance is limited by autofluorescence from the dye. Through the detection of a BK virus polymerase chain reaction (PCR) product, we demonstrate that the dye-doped PDMS system is an order of magnitude more sensitive than a similar undoped system (SNR: 138 vs. 9) without the use of any external optical filters at the detector.

Ultrasensitive PCR and real-time detection from human genomic samples using a bidirectional flow microreactor

In this paper we present a reliable bidirectional flow DNA amplification microreactor for processing real-world genomic samples. This system shares the low-power thermal responsiveness of a continuous flow reactor with the low surface area to volume ratio character of stationary reactors for reducing surface inhibitory effects. Silanization with dimethyldichlorosilane in combination with dynamic surface passivation was used to enhance PCR compatibility and enable efficient amplification. For real-time fragment amplification monitoring we have implemented an epimodal fluorescent detection capability. The passivated bidirectional flow system was ultrasensitive, achieving an RNase P gene detection limit of 24 human genome copies with a reaction efficiency of 77%. This starts to rival the performance of a conventional real-time PCR instrument with a reaction efficiency of 93% and revitalizes flow-through PCR as a viable component of lab on a chip DNA analysis formats.

Total nucleic acid analysis integrated on microfluidic devices

The design and integration of microfluidic devices for on-chip amplification of nucleic acids from various biological samples has undergone extensive development. The actual benefit to the biological community is far from clear, with a growing, but limited, number of application successes in terms of a full on-chip integrated analysis. Several advances have been made, particularly with the integration of amplification and detection, where amplification is most often the polymerase chain reaction. Full integration including sample preparation remains a major obstacle for achieving a quantitative analysis. We review the recently described devices incorporating in vitro gene amplification and compare devices relative to each other and in terms of fully achieving a miniaturised total analysis system (micro-TAS).

Rapid fabrication of a microfluidic device with integrated optical waveguides for DNA fragment analysis

The fabrication and performance of a microfluidic device with integrated liquid-core optical waveguides for laser induced fluorescence DNA fragment analysis is presented. The device was fabricated through poly(dimethylsiloxane) (PDMS) soft lithography and waveguides are formed in dedicated channels through the addition of a liquid PDMS pre-polymer of higher refractive index. Once a master has been fabricated, microfluidic chips can be produced in less than 3 h without the requirement for a cleanroom, yet this method provides an optical system that has higher performance than a conventional confocal optical assembly. Optical coupling was achieved through the insertion of optical fibers into fiber-to-waveguide couplers at the edge of the chip and the liquid-fiber interface results in low reflection and scattering losses. Waveguide propagation losses are measured to be 1.8 dB cm(-1) (532 nm) and 1.0 dB cm(-1) (633 nm). The chip displays an average total coupling loss of 7.6 dB due to losses at the optical fiber interfaces. In the electrophoretic separation and detection of a BK virus PCR product, the waveguide system achieves an average signal-to-noise ratio of 570 +/- 30 whereas a commercial confocal benchtop electrophoresis system achieves an average SNR of 330 +/- 30. To our knowledge, this is the first time that a waveguide-based system has been demonstrated to have a SNR comparable to a commercially available confocal-based system for microchip capillary electrophoresis.

High resolution DNA separations using microchip electrophoresis

Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.

Microfluidic chips for detecting the t(4;14) translocation and monitoring disease during treatment using reverse transcriptase-polymerase chain reaction analysis of IgH-MMSET hybrid transcripts

Diagnosis platforms incorporating low-cost microfluidic chips enable sensitive, rapid, and accurate genetic analysis that could facilitate customized therapies tailored to match the vulnerabilities of any types of cancer. Using ex vivo cancer cells, we have detected the unique molecular signature and a chromosomal translocation in multiple myeloma. Multiple myeloma is characterized by IgH rearrangements and translocations that enable unequivocal identification of malignant cells, detected here with integrated microfluidic chips incorporating genetic amplification via reverse transcriptase-polymerase chain reaction and capillary electrophoresis. On microfluidic chips, we demonstrated accurate and versatile detection of molecular signatures in individual cancer cells, with value for monitoring response to therapy, detecting residual cancer cells that mediate relapse, and evaluating prognosis. Thus, testing for two clinically important molecular biomarkers, the IgH VDJ signature and hybrid transcripts signaling the t(4;14) chro-mosomal translocation, with predictive value in diagnosis, treatment decisions, and monitoring has been efficiently implemented on a miniaturized microfluidic system.

Microfluidic platform for single nucleotide polymorphism genotyping of the thiopurine S-methyltransferase gene to evaluate risk for adverse drug events

Prospective clinical pharmacogenetic testing of the thiopurine S-methyltransferase gene remains to be realized despite the large body of evidence demonstrating clinical benefit for the patient and cost effectiveness for health care systems. We describe an entirely microchip-based method to genotype for common single nucleotide polymorphisms in the thiopurine S-methyltransferase gene that lead to serious adverse drug reactions for patients undergoing thiopurine therapy. Restriction fragment length polymorphism and allele-specific polymerase chain reaction have been adapted to a microfluidic chip-based polymerase chain reaction and capillary electrophoresis platform to genotype the common *2, *3A, and *3C functional alleles. In total, 80 patients being treated with thiopurines were genotyped, with 100% concordance between microchip and conventional methods. This is the first report of single nucleotide polymorphism detection using portable instrumentation and represents a significant step toward miniaturized for personalized treatment and automated point-of-care testing.

Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends

The possibility of performing fast and small-volume nucleic acid amplification and analysis on a single chip has attracted great interest. Devices based on this idea, referred to as micro total analysis, microfluidic analysis, or simply 'Lab on a chip' systems, have witnessed steady advances over the last several years. Here, we summarize recent research on chip substrates, surface treatments, PCR reaction volume and speed, architecture, approaches to eliminating cross-contamination and control and measurement of temperature and liquid flow. We also discuss product-detection methods, integration of functional components, biological samples used in PCR chips, potential applications and other practical issues related to implementation of lab-on-a-chip technologies.

Micropumps, microvalves, and micromixers within PCR microfluidic chips: Advances and trends

This review surveys the advances of microvalves, micropumps, and micromixers within PCR microfluidic chips over the past ten years. First, the types of microvalves in PCR chips are discussed, including active and passive microvalves. The active microvalves are subdivided into mechanical (thermopneumatic and shape memory alloy), non-mechanical (hydrogel, sol-gel, paraffin, and ice), and external (modular built-in, pneumatic, and non-pneumatic) microvalves. The passive microvalves also include mechanical (in-line polymerized gel and passive plug) and non-mechanical (hydrophobic) microvalves. The review then discusses mechanical (piezoelectric, pneumatic, and thermopneumatic) and non-mechanical (electrokinetic, magnetohydrodynamic, electrochemical, acoustic-wave, surface tension and capillary, and ferrofluidic magnetic) micropumps in PCR chips. Next, different micromixers within PCR chips are presented, including passive (Y/T-type flow, recirculation flow, and drop) and active (electrokinetically-driven, acoustically-driven, magnetohydrodynamical-driven, microvalves/pumps) micromixers. Finally, general discussions on microvalves, micropumps, and micromixers for PCR chips are given. The microvalve/micropump/micromixers allow high levels of PCR chip integration and analytical throughput.