Emerging optofluidic technologies for point-of-care genetic analysis systems: a review

Polymerase Chain Reaction Chips for Biomarker Discovery and Validation in Drug Development

Polymerase chain reaction (PCR) chips are advanced, microfluidic platforms that have revolutionized biomarker discovery and validation because of their high sensitivity, specificity, and throughput levels. These chips miniaturize traditional PCR processes for the speed and precision of nucleic acid biomarker detection relevant to advancing drug development. Biomarkers, which are useful in helping to explain disease mechanisms, patient stratification, and therapeutic monitoring, are hard to identify and validate due to the complexity of biological systems and the limitations of traditional techniques. The challenges to which PCR chips respond include high-throughput capabilities coupled with real-time quantitative analysis, enabling researchers to identify novel biomarkers with greater accuracy and reproducibility. More recent design improvements of PCR chips have further expanded their functionality to also include digital and multiplex PCR technologies. Digital PCR chips are ideal for quantifying rare biomarkers, which is essential in oncology and infectious disease research. In contrast, multiplex PCR chips enable simultaneous analysis of multiple targets, therefore simplifying biomarker validation. Furthermore, single-cell PCR chips have made it possible to detect biomarkers at unprecedented resolution, hence revealing heterogeneity within cell populations. PCR chips are transforming drug development, enabling target identification, patient stratification, and therapeutic efficacy assessment. They play a major role in the development of companion diagnostics and, therefore, pave the way for personalized medicine, ensuring that the right patient receives the right treatment. While this tremendously promising technology has exhibited many challenges regarding its scalability, integration with other omics technologies, and conformity with regulatory requirements, many still prevail. Future breakthroughs in chip manufacturing, the integration of artificial intelligence, and multi-omics applications will further expand PCR chip capabilities. PCR chips will not only be important for the acceleration of drug discovery and development but also in raising the bar in improving patient outcomes and, hence, global health care as these technologies continue to mature.

Opto-microfluidic coupling between optical waveguides and tilted microchannels in lithium niobate

This work presents a reconfigurable opto-microfluidic coupling between optical waveguides and tilted microfluidic channels in monolithic lithium niobate crystal. The light path connecting two waveguide arrays located on opposite sides of a microfluidic channel depends on the refractive index between the liquid phase and the hosting crystal. As a result, the optical properties of the flowing fluid, which is pumped into the microfluidic channel on demand, can be exploited to control the light pathways inside the optofluidic device. Proof-of-concept applications are herein presented, including microfluidic optical waveguide switching, optical refractive index sensing, and wavelength demultiplexing.

Micro-optics for microfluidic analytical applications

This critical review summarizes the developments in the integration of micro-optical elements with microfluidic platforms for facilitating detection and automation of bio-analytical applications.

Optofluidic Lab-on-a-Chip Fluorescence Sensor Using Integrated Buried ARROW (bARROW) Waveguides

Optofluidic, lab-on-a-chip fluorescence sensors were fabricated using buried anti-resonant reflecting optical waveguides (bARROWs). The bARROWs are impervious to the negative water absorption effects that typically occur in waveguides made using hygroscopic, plasma-enhanced chemical vapor deposition (PECVD) oxides. These sensors were used to detect fluorescent microbeads and had an average signal-to-noise ratio (SNR) that was 81.3% higher than that of single-oxide ARROW fluorescence sensors. While the single-oxide ARROW sensors were annealed at 300 °C to drive moisture out of the waveguides, the bARROW sensors required no annealing process to obtain a high SNR.

A Perspective on the Rise of Optofluidics and the Future

In the recent past, the field of optofluidics has thrived from the immense efforts of researchers from diverse communities. The concept of optofluidics combines optics and microfluidics to exploit novel properties and functionalities. In the very beginning, the unique properties of liquid, such as mobility, fungibility and deformability, initiated the motivation to develop optical elements or functions using fluid interfaces. Later on, the advancements of microelectromechanical system (MEMS) and microfluidic technologies enabled the realization of optofluidic components through the precise manipulation of fluids at microscale thus making it possible to streamline complex fabrication processes. The optofluidic system aims to fully integrate optical functions on a single chip instead of using external bulky optics, which can consequently lower the cost of system, downsize the system and make it promising for point-of-care diagnosis. This perspective gives an overview of the recent developments in the field of optofluidics. Firstly, the fundamental optofluidic components will be discussed and are categorized according to their basic working mechanisms, followed by the discussions on the functional instrumentations of the optofluidic components, as well as the current commercialization aspects of optofluidics. The paper concludes with the critical challenges that might hamper the transformation of optofluidic technologies from lab-based procedures to practical usages and commercialization.

Random lasing at the edge of a TiO2 nanotube thin film

In this paper, we introduce a random laser in which lasing action is observed at the edge of a dye-doped TiO₂ thin film. A TiO₂ nanotube membrane serves as a disordered structure that enhances the optical multiple scattering effect, while Rhodamine 6G dissolved in ethylene glycol is used as a gain medium. In the experiment, a random laser with a low threshold is observed when optically pumped at the fringe of a TiO₂ nanotube membrane, which makes it practical for microfluidic integration. Simulation results show that multiple scattered light between the nanotubes and ethylene glycol solution is more likely to form a resonance loop with the help of a random edge structure. This well interrupted the appearance of coherent spikes in the emission laser spectrum in the experiment. The edge random laser offers simplicity and convenience in both fabrication and operation, which makes it a promising component for optofluidic laser integration with TiO₂ functional material.

Optofluidic Device Based Microflow Cytometers for Particle/Cell Detection: A Review

Optofluidic devices combining micro-optical and microfluidic components bring a host of new advantages to conventional microfluidic devices. Aspects, such as optical beam shaping, can be integrated on-chip and provide high-sensitivity and built-in optical alignment. Optofluidic microflow cytometers have been demonstrated in applications, such as point-of-care diagnostics, cellular immunophenotyping, rare cell analysis, genomics and analytical chemistry. Flow control, light guiding and collecting, data collection and data analysis are the four main techniques attributed to the performance of the optofluidic microflow cytometer. Each of the four areas is discussed in detail to show the basic principles and recent developments. 3D microfabrication techniques are discussed in their use to make these novel microfluidic devices, and the integration of the whole system takes advantage of the miniaturization of each sub-system. The combination of these different techniques is a spur to the development of microflow cytometers, and results show the performance of many types of microflow cytometers developed recently.

Enhancement of binding kinetics on affinity substrates by laser point heating induced transport

Binding of analyte to an affinity substrate is significantly enhanced by laser point heating induced transport.

Point-of-care molecular diagnostic devices: an overview

Point-of-care molecular diagnostic devices are a rapidly expanding market. A variety of technologies are being developed for DNA detection and amplification, mostly aiming to detect pathogens. Of the two devices for detection of human genetic variations, both focus on CYP2C19 and have obtained regulatory approval. Most other devices have not obtained US FDA approval and are still undergoing clinical trials. Most, if not all, devices in development require equipment to which disposable test cartridges are placed. Thus, they may not fulfill FDA's definition of being 'simple'. There is a clear need to develop completely disposable devices that do not require equipment maintenance, and to detect other genetic variants predictive of disease susceptibility and drug response.

Development of a complete plasmonic grating-based sensor and its application for self-assembled monolayer detection

This work presents an integrated plasmonic biosensing device consisting of a one-dimensional metallic lamellar grating designed to exploit extraordinary transmission of light toward an underlying silicon photodetector. By means of finite element simulations, the grating parameters have been optimized to maximize the light transmission variation induced by the functionalization of the gold nanostructures. An optimized grating was fabricated using an electron beam process and an optoelectronic test bench suitable for sample tests was developed. A clear difference in the grating transmitted light due to surface functionalization was observed in presence of TM polarized illumination.

Surface plasmon resonance applications in clinical analysis

In the last 20 years, surface plasmon resonance (SPR) and its advancement with imaging (SPRi) emerged as a suitable and reliable platform in clinical analysis for label-free, sensitive, and real-time monitoring of biomolecular interactions. Thus, we report in this review the state of the art of clinical target detection with SPR-based biosensors in complex matrices (e.g., serum, saliva, blood, and urine) as well as in standard solution when innovative approaches or advanced instrumentations were employed for improved detection. The principles of SPR-based biosensors are summarized first, focusing on the physical properties of the transducer, on the assays design, on the immobilization chemistry, and on new trends for implementing system analytical performances (e.g., coupling with nanoparticles (NPs). Then we critically review the detection of analytes of interest in molecular diagnostics, such as hormones (relevant also for anti-doping control) and biomarkers of interest in inflammatory, cancer, and heart failure diseases. Antibody detection is reported in relation to immune disorder diagnostics. Subsequently, nucleic acid targets are considered for revealing genetic diseases (e.g., point mutation and single nucleotides polymorphism, SNPs) as well as new emerging clinical markers (microRNA) and for pathogen detection. Finally, examples of pathogen detection by immunosensing were also analyzed. A parallel comparison with the reference methods was duly made, indicating the progress brought about by SPR technologies in clinical routine analysis.

Light-governed capillary flow in microfluidic systems

Light-based flow systems for point-of-care devices are of interest because, in principle, sunlight could be used to operate them, potentially allowing for high functionality with minimal device complexity and expense. A light-operated method to drive flow using poly(N-isopropylacrylamide), a 'smart' polymer that changes wettability as a function of temperature, is introduced. It is grafted onto a carbon black-polydimethylsiloxane surface, which converts light into a thermal pattern that valves flow at user-defined locations. Flow rates are demonstrated ranging from 4 μL min(-1) at 25 °C to 0.1 μL min(-1) at 40 °C. The valving dynamics are also characterised, and a response time of less than 4 s is shown. Light-operated flow could provide the simple architecture and advanced functionality needed in low-resource point-of-care devices.

Single-step holographic fabrication of large-area periodically corrugated metal films

We have developed a simple, high-throughput, and cost-effective method to fabricate one-dimensional and two-dimensional periodically corrugated silver films over centimeter scale areas. This fabrication uses a single-step holographic patterning technique with laser intensities as low as 88.8 mW/cm(2) to deposit silver nanoparticles directly from solution to create gratings with periodicities of 570 nm. A dip in the transmission spectrum for these samples is observed due to certain visible wavelengths coupling to surface plasmon polaritons (SPPs) and the peak wavelength of this dip has a linear relationship with the surrounding material's refractive index (RI) with a sensitivity of 553.4 nm/RIU. The figure of merit (the ratio of refractive index sensitivity to the full width at half maximum (FWHM)) is typically in the range of 12-23. Our technique enables single-step fabrication of uniform, sub-wavelength periodic metal structures over a large area with low cost. Such sub-wavelength periodic metal structures are promising candidates as disposable sensors in applications such as affordable environmental monitoring systems and point-of-care diagnostics.

Non-emissive plastic colour filters for fluorescence detection

We report the fabrication of non-emissive short- and long-pass filters on plastic for high sensitivity fluorescence detection. The filters were prepared by overnight immersion of titania-coated polyethylene terephthalate (PET) in an appropriate dye solution - xylene cyanol for short-pass filtering and fluorescein disodium salt for long-pass filtering - followed by repeated washing to remove excess dye. The interface between the titania and the dye molecule induces efficient quenching of photo-generated excitons in the dye molecule, reducing auto-fluorescence to negligible values and so overcoming the principal weakness of conventional colour filters. Using the filters in conjunction with a 505 nm cyan light-emitting diode and a Si photodiode, dose-response measurements were made for T8661 Transfluosphere beads in the concentration range 1 × 10(9) to 1 × 10(5) beads μL(-1), yielding a limit of detection of 3 × 10(4) beads μL(-1). The LED/short-pass filter/T8661/long-pass filter/Si-photodiode combination reported here offers an attractive solution for sensitive, low cost fluorescence detection that is readily applicable to a wide range of bead-based immunodiagnostic assays.

A point-of-care PCR test for HIV-1 detection in resource-limited settings

A low-cost, fully integrated sample-to-answer, quantitative PCR (qPCR) system that can be used for detection of HIV-1 proviral DNA in infants at the point-of-care in resource-limited settings has been developed and tested. The system is based on a novel DNA extraction method, which uses a glass fiber membrane, a disposable assay card that includes on-board reagent storage, provisions for thermal cycling and fluorescence detection, and a battery-operated portable analyzer. The system is capable of automated PCR mix assembly using a novel reagent delivery system and performing qPCR. HIV-1 and internal control targets are detected using two spectrally separated fluorophores, FAM and Quasar 670. In this report, a proof-of-concept of the platform is demonstrated. Initial results with whole blood demonstrate that the test is capable of detecting HIV-1 in blood samples containing greater than 5000 copies of HIV-1. In resource-limited settings, a point-of-care HIV-1 qPCR test would greatly increase the number of test results that reach the infants caregivers, allowing them to pursue anti-retroviral therapy.

Cervical smear photodiagnosis by fluorescence

OBJECTIVE

Fluorescence is widely investigated and can characterize general changes occurring in the state of the cell and the tissue during physiological and/or pathological processes, but the method has not been adopted for clinical use. We present a photodiagnostic device and a relevant evaluation method fitted to classical screening procedures. This method is based on the discovery of smear content intrinsic fluorescent markers.

BACKGROUND DATA

Meaningful spectral components of cervical smear samples differ from those measured in the entire live cervix. This article deals with the identification of changes in smear spectra in cervicitis and CIN2+ (cervical intraepithelial neoplasia of the second degree or higher) at 355 nm excitation.

METHODS

Methods used in the study: microlaser-induced fluorescence spectroscopy of liquid cytology samples and histological evaluation of the biopsies of the same cervix (and/or only cytological evaluation) was performed for 78 cases. The fluorescence spectra of cervical cytology supernatant sediment were approximated with several Gaussian components. The ratios of the area under each Gaussian component to the whole area under the experimental curve were calculated and compared among histological groups by using the Mann-Whitney test and receiver operating characteristic (ROC) analysis.

RESULTS

The results of this study are a concise summary of the essential features verified by the data: the spectral regions 402-416 nm and 424-438 nm are important for the discrimination of both normal and CIN2+ groups (in terms of sensitivity, specificity, and positive predictive value). The spectral regions 480-515 nm and 595-625 nm are important for the identification of cervicitis.

CONCLUSIONS

Cervical smear autofluorescence diagnostics could be useful for cancer screening at the point of care, in a simple cytology laboratory, and for the monitoring of treatment. We suggest possible fluorophores in the smear content.

All-optical diffractive/transmissive switch based on coupled cycloidal diffractive waveplates

Pairs of cycloidal diffractive waveplates can be used to doubly diffract or collinearly propagate laser radiation of the appropriate wavelength. The use of a dynamic phase retarder placed in between the pair can be utilized to switch between the two optical states. We present results from the implementation of an azo-based retarder whose optical properties can be modulated using light itself. We show fast and efficient switching between the two states for both CW and single nanosecond laser pulses of green radiation. Contrasts greater than 100:1 were achieved. The temporal response as a function of light intensity is presented and the optical switching is shown to be polarization independent.

Microfluidic technology for molecular diagnostics

Molecular diagnostics have helped to improve the lives of millions of patients worldwide by allowing clinicians to diagnose patients earlier as well as providing better ongoing therapies. Point-of-care (POC) testing can bring these laboratory-based techniques to the patient in a home setting or to remote settings in the developing world. However, despite substantial progress in the field, there still remain many challenges. Progress in molecular diagnostics has benefitted greatly from microfluidic technology. This chapter aims to summarise the more recent advances in microfluidic-based molecular diagnostics. Sections include an introduction to microfluidic technology, the challenges of molecular diagnostics, how microfluidic advances are working to solve these issues, some alternative design approaches, and detection within these systems.

Bioinspired colloidal photonic crystals with controllable wettability

Because of the combinatorial advantage of their unique light manipulation properties and potential applications in novel optical devices, colloidal photonic crystals (PCs), the periodic arrangement of monodispersed latex spheres, have attracted interest from researchers. In particular, colloidal PCs exhibit structural colors based on interference effects within their periodic structures. The wavelength of these colors lies in the visible range, making them particularly attractive for a variety of applications. Colloidal PCs are extensively used in templating, catalysis, and chromatographic separations. Inspired by biological PCs with both structural color and specific wettability, researchers have fabricated colloidal PCs with controllable wettability as described in this Account. The wettability can be adjusted by the intrinsic roughness of colloidal crystals in combination with the tunable chemical composition of latex surfaces. Changes in the chemical composition of the latex surface under external stimuli, such as light, electricity, and heat, can reversibly control the wettability of PCs. Furthermore, the hierarchical structure of latex particles can effectively alter the water adhesive force of superhydrophobic colloidal PCs. Patterned PCs with a variety of wettabilities can be assembled using inkjet printing from well-designed latex suspensions. By combining their structural color and specific wettability, we also exemplify some of the promising applications of colloidal PCs as templates for the construction of hierarchical structures, as indicators for controllable transport of liquid droplets, and as color-based sensors for the monitoring changes in their environment. These findings offer innovative insights into the design of novel colloidal PCs and will be of great importance for further applications of these materials.

Non-emissive colour filters for fluorescence detection

We describe a simple technique for fabricating non-emissive colour filters based on the sensitisation of a highly porous nanostructured metal-oxide film with a monolayer of dye molecules. Ultrafast electron transfer at the oxide/dye interface induces efficient quenching of photogenerated excitons in the dye, reducing the photoluminescence quantum yield by many orders of magnitude. The resultant filters exhibit much less autofluorescence than conventional colour filters (where the chromophore is dispersed in a glass or polymer host), and are a viable low cost alternative to interference filters for microfluidic devices and other applications requiring non-emissive filtering.

Surface plasmon resonance biosensor for parallelized detection of protein biomarkers in diluted blood plasma

Surface plasmon resonance (SPR) biosensor for high-throughput screening of protein biomarkers in diluted blood plasma is reported. The biosensor combines a high-resolution SPR imaging sensor and a high-density protein array with low-fouling background. The SPR imaging sensor utilizes polarization contrast and advanced referencing and provides a total of 120 sensing areas (each 200 μm×150 μm). Antibodies are immobilized on the sensing areas via hybridization of antibody-oligonucleotide conjugates to thiolated complementary oligonucleotides microspotted on the sensor surface (DNA-directed immobilization). A low-fouling background is achieved by covalent immobilization of bovine serum albumin to carboxyl-terminated thiols filling the areas among the thiolated oligonucleotides and outside the sensing areas. The biosensor was evaluated for detection of protein biomarkers relevant to cancer diagnostics--human chorionic gonadotropin (hCG) and activated leukocyte cell adhesion molecule (ALCAM) both in buffer and in 10% blood plasma. Limits of detection as low as 45 ng/mL (ALCAM) and 100 ng/mL (hCG) were achieved in blood plasma samples.

Lensless CCD-based fluorometer using a micromachined optical Söller collimator

In this paper, we describe a simple charge-coupled device (CCD) based lensless fluorometer with sensitivity in the range of current ELISA plate readers. In our lensfree fluorometer, a multi-wavelength LED light source was used for fluorophore excitation. To collimate the light, we developed a simple optical Söller collimator based on a "stack of pinholes" (a stack of black PMMA with array of pinholes machined with laser) enabling the light to be collimated from the LED through the filters and the assay's microfluidics directly onto the CCD without a lens. The elimination of the lens that is used in almost all other current CCD based detection systems has four major advantages: (1) It simplifies the device design and fabrication while reducing cost. (2) It reduces the distance between the sample and the measuring device (without a lens the distance needed to focus the image on the CCD is reduced and the fluorometer can be more compact). (3) It couples the CCD and the detected surface by using an optical Söller Collimator which allows the use of filters for fluorescence detection. (4) It also uncouples the CCD and the microfluidics to enable the use of interchangeable fluidics while protecting the delicate CCD. The lensless CCD-based fluorometer is capable of detecting 16 samples simultaneously, and was used for in vitro detection of botulinum neurotoxin serotype A (BoNT-A) activity with a FRET assay that measures cleavage of a fluorophore-tagged peptide substrate specific for BoNT-A (SNAP-25) by the toxin light chain (LcA). The limit of detection (LOD) of our lensless fluorometer is 1.25 nM, which is similar to the LOD of a modern ELISA plate reader. Combined with microfluidics, this simple low cost point-of-care (POC) medical diagnostic system may be useful for the performance of many other complex medical diagnostic assays without a laboratory and thus potentially enhancing the accessibility and the quality of health care delivery in underserved populations.

Miniaturized lensless imaging systems for cell and microorganism visualization in point-of-care testing

Low-cost, robust, and user-friendly diagnostic capabilities at the point-of-care (POC) are critical for treating infectious diseases and preventing their spread in developing countries. Recent advances in micro- and nanoscale technologies have enabled the merger of optical and fluidic technologies (optofluidics) paving the way for cost-effective lensless imaging and diagnosis for POC testing in resource-limited settings. Applications of the emerging lensless imaging technologies include detecting and counting cells of interest, which allows rapid and affordable diagnostic decisions. This review presents the advances in lensless imaging and diagnostic systems, and their potential clinical applications in developing countries. The emerging technologies are reviewed from a POC perspective considering cost effectiveness, portability, sensitivity, throughput and ease of use for resource-limited settings.

Diagnosing infections--current and anticipated technologies for point-of-care diagnostics and home-based testing

In recent years, we have witnessed many transitions in healthcare systems around the globe. For example, population expansion and ageing, and the human immunodeficiency virus (HIV)-AIDS epidemics, have exerted pressure to decentralize the practice of healthcare outside of traditional settings to bring care to those in need. Upstream of patient management, diagnosis is aimed at adequately orienting medical decisions, and considerable efforts have been made to make this process faster and more efficient. However, there are several diseases and medical conditions that may/will benefit from technologies and tests that can be performed closer to the patient, at the point of care or even in the home. In this review, and in light of the paradox that technology and assay developers and healthcare officials must take into consideration for advancing human health in developed and developing countries, we present an overview of rapid diagnosis of infectious diseases at the point of care and of technologies that may contribute to enhancement of the worldwide point-of-care testing market.

Microfluidics in macro-biomolecules analysis: macro inside in a nano world

Use of microfluidic devices in the life sciences and medicine has created the possibility of performing investigations at the molecular level. Moreover, microfluidic devices are also part of the technological framework that has enabled a new type of scientific information to be revealed, i.e. that based on intensive screening of complete sets of gene and protein sequences. A deeper bioanalytical perspective may provide quantitative and qualitative tools, enabling study of various diseases and, eventually, may offer support for the development of accurate and reliable methods for clinical assessment. This would open the way to molecule-based diagnostics, i.e. establish accurate diagnosis and disease prognosis based on identification and/or quantification of biomacromolecules, for example proteins or nucleic acids. Finally, the development of disposable and portable devices for molecule-based diagnosis would provide the perfect translation of the science behind life-science research into practical applications dedicated to patients and health practitioners. This review provides an analytical perspective of the impact of microfluidics on the detection and characterization of bio-macromolecules involved in pathological processes. The main features of molecule-based diagnostics and the specific requirements for the diagnostic devices are discussed. Further, the techniques currently used for testing bio-macromolecules for potential diagnostic purposes are identified, emphasizing the newest developments. Subsequently, the challenges of this type of application and the status of commercially available devices are highlighted, and future trends are noted.

Implantable semiconductor biosensor for continuous in vivo sensing of far-red fluorescent molecules

We have fabricated miniature implantable fluorescence sensors for continuous fluorescence sensing applications in living subjects. These monolithically integrated GaAs-based sensors incorporate a 675 nm vertical-cavity surface-emitting laser (VCSEL), a GaAs PIN photodiode, and a fluorescence emission filter. We demonstrate high detection sensitivity for Cy5.5 far-red dye (50 nanoMolar) in living tissue, limited by the intrinsic background autofluorescence. These low cost, sensitive and scalable sensors are promising for long-term continuous monitoring of molecular dynamics for biomedical studies in freely moving animals.

Tailored electroactive and quantitative ligand density microarrays applied to stem cell differentiation

The ability to precisely control the interactions between materials and mammalian cells at the molecular level is crucial to understanding the fundamental chemical nature of how the local environment influences cellular behavior as well as for developing new biomaterials for a range of biotechnological and tissue engineering applications. In this report, we develop and apply for the first time a quantitative electroactive microarray strategy that can present a variety of ligands with precise control over ligand density to study human mesenchymal stem cell (hMSC) differentiation on transparent surfaces with a new method to quantitate adipogenic differentiation. We found that both the ligand composition and ligand density influence the rate of adipogenic differentiation from hMSC's. Furthermore, this new analytical biotechnology method is compatible with other biointerfacial characterization technologies (surface plasmon resonance, mass spectrometry) and can also be applied to investigate a range of protein-ligand or cell-material interactions for a variety of systems biology studies or cell behavior based assays.