Fully automatic integrated continuous-flow digital PCR device for absolute DNA quantification

Development of a sensitive droplet digital PCR according to the HPV infection specificity in Chinese population

HPV16 and 18 are positively correlated with cervical carcinogenesis. However, HPV prevalence tends to vary according to region, nationality, and environment. The most prevalent high-risk (HR) HPV genotypes are HPV16, 52, 58, 56, 18, 33, and 45), while the low-risk (LR) genotypes are HPV6 and 11 in the Chinese population. Importantly, undetectable low-copy HPV DNA could be an important indicator of integration into the human genome and may be a precursor to cancer progression. The HPV viral load changes dramatically, either increasing or decreasing rapidly during carcinogenesis, and traditional quantitative real-time PCR (qPCR) cannot accurately capture this subtle change. Therefore, in this study, a reliable droplet digital PCR (ddPCR) method was developed to simultaneously detect and quantify HPV genotypes. The ddPCR quantitative results showed high accuracy, sensitivity, and specificity compared to qPCR results employing the same clinical specimens and supplemented the ddPCR assay for HPV52/56/58/6 genotypes according to the infection specificity of the Chinese population. In summary, this procedure is valuable for quantifying HPV DNA, especially under conditions of low template copy number in cervical intraepithelial neoplasia (CIN) and/or cervical cancer. Additionally, this method can dynamically observe the prognosis and outcome of HPV infection and thus be used as an effective means for real-time monitoring of tumor load.

Irregular Antibody Screening Using a Microdroplet Platform

The screening procedure for antibodies is considered the most tedious among the three pretransfusion operations, i.e., ABO and Rhesus (Rh) typing, irregular antibody screening/identification, and crossmatching tests. The commonly used screening method for irregular antibodies in clinics at present is a manual polybrene test (MP). The MP test involves numerous reagent replacement and centrifuge procedures, and the sample volume is expected to be relatively less. Herein, screening red blood cells (RBCs) and serum irregular antibodies are encapsulated in microdroplets with a diameter of ~300 μm for a hemagglutination reaction. Owing to the advantage of spatial limitation in microdroplets, screening RBCs and irregular antibodies can be directly agglutinated, thereby eliminating the need for centrifugation and the addition of reagents to promote agglutination, as required by the MP method. Furthermore, the results for a large number of repeated tests can be concurrently obtained, further simplifying the steps of irregular antibody screening and increasing accuracy. Eight irregular antibodies are screened using the proposed platform, and the results are consistent with the MP method. Moreover, the volume of blood samples and antibodies can be reduced to 10 μL and 5 μL, respectively, which is ten times less than that using the MP method.

Advances in Simple, Rapid, and Contamination-Free Instantaneous Nucleic Acid Devices for Pathogen Detection

Pathogenic pathogens invade the human body through various pathways, causing damage to host cells, tissues, and their functions, ultimately leading to the development of diseases and posing a threat to human health. The rapid and accurate detection of pathogenic pathogens in humans is crucial and pressing. Nucleic acid detection offers advantages such as higher sensitivity, accuracy, and specificity compared to antibody and antigen detection methods. However, conventional nucleic acid testing is time-consuming, labor-intensive, and requires sophisticated equipment and specialized medical personnel. Therefore, this review focuses on advanced nucleic acid testing systems that aim to address the issues of testing time, portability, degree of automation, and cross-contamination. These systems include extraction-free rapid nucleic acid testing, fully automated extraction, amplification, and detection, as well as fully enclosed testing and commercial nucleic acid testing equipment. Additionally, the biochemical methods used for extraction, amplification, and detection in nucleic acid testing are briefly described. We hope that this review will inspire further research and the development of more suitable extraction-free reagents and fully automated testing devices for rapid, point-of-care diagnostics.

A three-in-one microfluidic droplet digital PCR platform for absolute quantitative analysis of DNA

Droplet digital polymerase chain reaction (ddPCR) technology has found widespread applications in the ultrasensitive analysis of nucleic acids, where integrated ddPCR platforms with the capability of sample dispersion, followed by in situ amplification and data analysis, are highly expected. However, current integrated ddPCR platforms are usually limited by either difficultly mass-produced materials or lack of integrated control instruments, restricting their practical application. This paper proposes an integrated three-in-one ddPCR platform with high user-friendliness and practicability, which is composed of an easy-to-use chip and a matching control instrument. The chip was made of thermally resistant and easily mass-produced polycarbonate (PC) material, and the benchtop control instrument was designed to perform droplet generation, in situ amplification, and fluorescence reading. The droplet generation and in situ heating on the chip were well characterized. Finally, the performance of the platform was validated through the analysis of the EGFR L858R mutation in lung cancer. The proposed three-in-one ddPCR platform shows great practicability in ultrasensitive nucleic acid testing. By virtue of its sensitivity, practicability, and cost-effectiveness, the ddPCR can serve as a universal detection platform for monitoring nucleic acid in the fields of tumor diagnosis, pathogen detection, and prenatal diagnosis.

Recent Advances in Molecular and Immunological Diagnostic Platform for Virus Detection: A Review

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing coronavirus disease (COVID-19) outbreak and a rising demand for the development of accurate, timely, and cost-effective diagnostic tests for SARS-CoV-2 as well as other viral infections in general. Currently, traditional virus screening methods such as plate culturing and real-time PCR are considered the gold standard with accurate and sensitive results. However, these methods still require sophisticated equipment, trained personnel, and a long analysis time. Alternatively, with the integration of microfluidic and biosensor technologies, microfluidic-based biosensors offer the ability to perform sample preparation and simultaneous detection of many analyses in one platform. High sensitivity, accuracy, portability, low cost, high throughput, and real-time detection can be achieved using a single platform. This review presents recent advances in microfluidic-based biosensors from many works to demonstrate the advantages of merging the two technologies for sensing viruses. Different platforms for virus detection are classified into two main sections: immunoassays and molecular assays. Moreover, available commercial sensing tests are analyzed.

A Short Review on Miniaturized Biosensors for the Detection of Nucleic Acid Biomarkers

Even today, most biomarker testing is executed in centralized, dedicated laboratories using bulky instruments, automated analyzers, and increased analysis time and expenses. The development of miniaturized, faster, low-cost microdevices is immensely anticipated for substituting for these conventional laboratory-oriented assays and transferring diagnostic results directly onto the patient's smartphone using a cloud server. Pioneering biosensor-based approaches might make it possible to test biomarkers with reliability in a decentralized setting, but there are still a number of issues and restrictions that must be resolved before the development and use of several biosensors for the proper understanding of the measured biomarkers of numerous bioanalytes such as DNA, RNA, urine, and blood. One of the most promising processes to address some of the issues relating to the growing demand for susceptible, quick, and affordable analysis techniques in medical diagnostics is the creation of biosensors. This article critically discusses a short review of biosensors used for detecting nucleic acid biomarkers, and their use in biomedical prognostics will be addressed while considering several essential characteristics.

Hundreds-Dollar-Level Multiplex Integrated RT-qPCR Quantitative System for Field Detection

The COVID-19 pandemic poses a threat to global health. Due to its high sensitivity, specificity, and stability, real-time fluorescence quantitative (real-time PCR) detection has become the most extensively used approach for diagnosing SARS-CoV-2 pneumonia. According to a report from the World Health Organization, emerging and underdeveloped nations lack nucleic acid detection kits and polymerase chain reaction (PCR) instruments for molecular biological detection. In addition, sending samples to a laboratory for testing may result in considerable delays between sampling and diagnosis, which is not favorable to the timely prevention and control of new crown outbreaks. Concurrently, there is an urgent demand for accurate PCR devices that do not require a laboratory setting, are more portable, and are capable of completing testing on-site. Hence, we report on HDLRT-qPCR, a new, low-cost, multiplexed real-time fluorescence detection apparatus that we have developed for on-site testing investigations of diverse diseases in developing nations. This apparatus can complete on-site testing rapidly and sensitively. The entire cost of this instrument does not exceed USD 760. In order to demonstrate the applicability of our PCR instrument, we conducted testing that revealed that we achieved gradient amplification and melting curves comparable to those of commercially available equipment. Good consistency characterized the testing outcomes. The successful detection of target genes demonstrates the reliability of our inexpensive PCR diagnostic technique. With this apparatus, there is no need to transport samples to a central laboratory; instead, we conduct testing at the sampling site. This saves time on transportation, substantially accelerates overall testing speed, and provides results within 40 min.

Direct Chromosomal Phasing: An Easy and Fast Approach for Broadening Prenatal Diagnostic Applicability

The assignment of alleles to haplotypes in prenatal diagnostic assays has traditionally depended on family study analyses. However, this prevents the wide application of prenatal diagnosis based on haplotype analysis, especially in countries with dispersed populations. Here, we present an easy and fast approach using Droplet Digital PCR for the direct determination of haplotype blocks, overcoming the necessity for acquiring other family members’ genetic samples. We demonstrate this approach on nine families that were referred to our center for a prenatal diagnosis of β-thalassaemia using four highly polymorphic single nucleotide variations and the most common pathogenic β-thalassaemia variation in our population. Our approach resulted in the successful direct chromosomal phasing and haplotyping for all nine of the families analyzed, demonstrating a complete agreement with the haplotypes that are ascertained based on family trios. The clinical utility of this approach is envisaged to open the application of prenatal diagnosis for β-thalassaemia to all cases, while simultaneously providing a model for extending the prenatal diagnostic application of other monogenic diseases as well.

Importance of sample input volume for accurate SARS-CoV-2 qPCR testing

Nucleic acid testing is the most widely used detection method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Currently, a number of COVID-19 real-time quantitative reverse transcription PCR (qPCR) kits with high sensitivity and specificity are available for SARS-CoV-2 testing. However, these qPCR assays are not always reliable in detecting low viral load samples (Ct-value ≥ 35), resulting in inconclusive or false-negative results. Here, we used a Poisson distribution to illustrate the inconsistent performance of qPCR tests in detecting low viral load samples. From this, we concluded that the false-negative outcomes resulted from the random occurrences of sampling zero target molecules in a single test, and the probability to sample zero target molecules in one test decreased significantly with increasing purified RNA or initial sample input volume. At a given RNA concentration of 0.5 copy/μL, the probability of sampling zero RNA molecules decreased from 36.79% to close to 0.67% after increasing the RNA input volume from 2 to 10 μL. A SARS-CoV-2 qPCR assay with an LOD of 300 copies/mL was used to validate the improved consistency of the qPCR tests. We found that the false-negative qPCR results of clinical COVID-19 samples with a Ct ≥ 35 decreased by 50% after increasing the input of purified RNA from 2 to 10 μL. The consistency, accuracy, and robustness of nucleic acid testing for SARS-CoV-2 samples with low viral loads can be improved by increasing the sample input volume.

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR)‎ methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.