Rapid and label-free amplification and detection assay for genotyping of cancer biomarker

An ultraportable and versatile point-of-care DNA testing platform

Point-of-care testing (POCT) has broad applications in resource-limited settings. Here, a POCT platform termed POCKET (point-of-care kit for the entire test) is demonstrated that is ultraportable and versatile for analyzing multiple types of DNA in different fields in a sample-to-answer manner. The POCKET is less than 100 g and smaller than 25 cm in length. The kit consists of an integrated chip (i-chip) and a foldable box (f-box). The i-chip integrates the sample preparation with a previously unidentified, triple signal amplification. The f-box uses a smartphone as a heater, a signal detector, and a result readout. We detected different types of DNA from clinics to environment to food to agriculture. The detection is sensitive (<10³ copies/ml), specific (single-base differentiation), speedy (<2 hours), and stable (>10 weeks shelf life). This inexpensive, ultraportable POCKET platform may become a versatile sample-to-answer platform for clinical diagnostics, food safety, agricultural protection, and environmental monitoring.

Digital polymerase chain reaction technology - recent advances and future perspectives

Digital polymerase chain reaction (dPCR) technology has remained a "hot topic" in the last two decades due to its potential applications in cell biology, genetic engineering, and medical diagnostics. Various advanced techniques have been reported on sample dispersion, thermal cycling and output monitoring of digital PCR. However, a fully automated, low-cost and handheld digital PCR platform has not been reported in the literature. This paper attempts to critically evaluate the recent developments in techniques for sample dispersion, thermal cycling and output evaluation for dPCR. The techniques are discussed in terms of hardware simplicity, portability, cost-effectiveness and suitability for automation. The present paper also discusses the research gaps observed in each step of dPCR and concludes with possible improvements toward portable, low-cost and automatic digital PCR systems.

Whispering-Gallery Mode Resonators for Detecting Cancer

Optical resonators are sensors well known for their high sensitivity and fast response time. These sensors have a wide range of applications, including in the biomedical fields, and cancer detection is one such promising application. Sensor diagnosis currently has many limitations, such as being expensive, highly invasive, and time-consuming. New developments are welcomed to overcome these limitations. Optical resonators have high sensitivity, which enable medical testing to detect disease in the early stage. Herein, we describe the principle of whispering-gallery mode and ring optical resonators. We also add to the knowledge of cancer biomarker diagnosis, where we discuss the application of optical resonators for specific biomarkers. Lastly, we discuss advancements in optical resonators for detecting cancer in terms of their ability to detect small amounts of cancer biomarkers.

Applications of Optical Microcavity Resonators in Analytical Chemistry

Optical resonator sensors are an emerging class of analytical technologies that use recirculating light confined within a microcavity to sensitively measure the surrounding environment. Bolstered by advances in microfabrication, these devices can be configured for a wide variety of chemical or biomolecular sensing applications. We begin with a brief description of optical resonator sensor operation, followed by discussions regarding sensor design, including different geometries, choices of material systems, methods of sensor interrogation, and new approaches to sensor operation. Throughout, key developments are highlighted, including advancements in biosensing and other applications of optical sensors. We discuss the potential of alternative sensing mechanisms and hybrid sensing devices for more sensitive and rapid analyses. We conclude with our perspective on the future of optical microcavity sensors and their promise as versatile detection elements within analytical chemistry.

Two-stage sample-to-answer system based on nucleic acid amplification approach for detection of malaria parasites

Rapid, early, and accurate diagnosis of malaria is essential for effective disease management and surveillance, and can reduce morbidity and mortality associated with the disease. Although significant advances have been achieved for the diagnosis of malaria, these technologies are still far from ideal, being time consuming, complex and poorly sensitive as well as requiring separate assays for sample processing and detection. Therefore, the development of a fast and sensitive method that can integrate sample processing with detection of malarial infection is desirable. Here, we report a two-stage sample-to-answer system based on nucleic acid amplification approach for detection of malaria parasites. It combines the Dimethyl adipimidate (DMA)/Thin film Sample processing (DTS) technique as a first stage and the Mach-Zehnder Interferometer-Isothermal solid-phase DNA Amplification (MZI-IDA) sensing technique as a second stage. The system can extract DNA from malarial parasites using DTS technique in a closed system, not only reducing sample loss and contamination, but also facilitating the multiplexed malarial DNA detection using the fast and accurate MZI-IDA technique. Here, we demonstrated that this system can deliver results within 60min (including sample processing, amplification and detection) with high sensitivity (<1 parasite μL(-1)) in a label-free and real-time manner. The developed system would be of great potential for better diagnosis of malaria in low-resource settings.

Rapid and reliable genotyping of HLA-B*58:01 in four Chinese populations using a single-tube duplex real-time PCR assay

AIM

HLA-B*58:01 is strongly associated with allopurinol-induced severe cutaneous adverse reactions. This study aimed to develop a new and convenient method for HLA-B*58:01 genotyping and to investigate HLA-B*58:01 distribution in different Chinese populations.

MATERIALS & METHODS

Combining of sequence-specific primers and TaqMan probe, a single-tube duplex real-time PCR assay for HLA-B*58:01 typing was established.

RESULTS

The HLA-B*58:01 genotyping result in Buyei (n = 100) by real-time PCR showed 100% concordance with those by sequence-based typing. The prevalence of HLA-B*58:01 carrier in Buyei (17%, n = 100) was significantly higher than those in Northern Han (4%, n = 100), Tibetan (5.1%, n = 99) and Uighur (2%, n = 50) populations (p < 0.05).

CONCLUSION

The newly developed reliable assay was appropriate for HLA-B*58:01 detection prior to allopurinol administration in clinical settings.

LoMA-B: a simple and versatile lab-on-a-chip system based on single-channel bisulfite conversion for DNA methylation analysis

Miniaturized lab-on-a-chip (LOC) systems have been developed for genetic and epigenetic analyses in clinical applications because of advantages such as reduced sample size and reagent consumption, rapid processing speed, simplicity, and enhanced sensitivity. Despite tremendous efforts made towards developing LOC systems for use in the clinical setting, the development of LOC systems to analyze DNA methylation, which is an emerging epigenetic marker causing the abnormal silencing of genes including tumor suppressor genes, is still challenging because of the gold standard methods involving a bisulfite conversion step. Existing bisulfite conversion-based techniques are not suitable for clinical use due to their long processing time, labor intensiveness, and the purification steps involved. Here, we present a lab-on-a-chip system for DNA methylation analysis based on bisulfite conversion (LoMA-B), which couples a sample pre-processing module for on-chip bisulfite conversion and a label-free, real-time detection module for rapid analysis of DNA methylation status using an isothermal DNA amplification/detection technique. The methylation status of the RARβ gene in human genomic DNA extracted from MCF-7 cells was analyzed by the LoMA-B system within 80 min (except 16 h for sensor preparation) compared to conventional MS-PCR within 24 h. Furthermore, the LoMA-B system is highly sensitive and can detect as little as 1% methylated DNA in a methylated/unmethylated cell mixture. Therefore, the LoMA-B system is an efficient diagnostic tool for the simple, versatile, and quantitative evaluation of DNA methylation patterns for clinical applications.

A rapid MZI-IDA sensor system for EGFR mutation testing in non-small cell lung cancer (NSCLC)

Epidermal growth factor receptor (EGFR) is a non-small-cell lung cancer biomarker, based on which several near-patient-testing methods have been developed and applied to predict treatment response on individual patients. Existing methods for detection of EGFR mutation are costly, labor-intensive and time-consuming. In this paper, we report a novel EGFR mutation testing system, which is based on Mach-Zehnder Interferometer (MZI) sensor and isothermal solid-phase DNA amplification (IDA) technique, called MZI-IDA sensor system. The system can deliver results within 30 min and shows high sensitivity to detect trace amounts of genomic DNA (<1 copy). In addition, the system is able to detect a L858R mutation in a 99:1 mixture of wild-type and mutant cells. In a pilot clinical study, the system is compared with conventional methods (PCR and direct sequencing) by using tissue biopsy samples from NSCLC patients. The MZI-IDA sensor system is proved to be capable of fast and accurate detection of the L858R mutation of EGFR gene in clinical samples. This may greatly help the clinicians develop an appropriate treatment plan.

Rapid nucleic acid detection of Zaire ebolavirus on paper fluidics

We presented a type of novel paper-based microfluidics for the rapid detection of Zaire ebolavirus.