Single-target Assays Research Articles

Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol.

The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borreliaceae are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnoses center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration of the causative spirochaetes and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the highly extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity as single target assays cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae lifecycle in which these parasites have to survive in multiple hosts each with unique immune responses. We constructed a Borreliaceae family-level pangenome and characterized the phylogenetic relationships among the constituent taxa which supports the recent taxonomy of splitting the family into at least two genera. Gene content pro les were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pangenome will enable precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.

Dual-potential encoded electrochemiluminescence for multiplexed gene assay with one luminophore as tag

Multiplexed gene assay for simultaneously detecting the multi-targets of nucleic acids is strongly anticipated for the accurate diseases diagnosis and prediction, and all commercial available gene assays for IVD are a kind of single-target assay. Herein, a dual-potential encoded and coreactant-free electrochemiluminescence (ECL) strategy is proposed for the multiplexed gene assay, which can be conveniently carried out by directly oxidizing the same luminescent tag of dual-stabilizers-capped CdTe nanocrystals (NCs). The CdTe NCs linked with sulfhydryl-RNA via Cd−S bond merely exhibits one ECL process around 0.32 V with a narrow triggering-potential-window of 0.35 V, while CdTe NCs linked with amino-RNA via amide linkage solely gives off one ECL process around 0.82 V with a narrow triggering-potential-window of 0.30 V. Multiplexing ECL of both sulfhydryl-RNA-functionalized CdTe NCs and amino-RNA-functionalized CdTe NCs can be utilized to simultaneously detect the open reading frame 1ab (ORF1ab) and the nucleoprotein (N) genes without crosstalk, in which ECL of sulfhydryl-RNA-functionalized CdTe NCs can dynamically determine ORF1ab from 200 aM to 10 fM with a limit of detection (LOD) of 100 aM, while ECL of amino-RNA-functionalized CdTe NCs can linearly detect N gene from 5 fM to 1 pM with a LOD of 2 fM. Post-engineering CdTe NCs with RNA in a labeling-bond engineering way would provide a potential-selective and encoded ECL strategy for multiplexed gene assay with one luminophore.

Evaluation of a Multiplex Bead Assay against Single-Target Assays for Detection of IgG Antibodies to SARS-CoV-2.

ABSTRACTSerological assays for SARS-CoV-2 antibodies must be validated for performance with a large panel of clinical specimens. Most existing assays utilize a single antigen target and may be subject to reduced diagnostic specificity. This study evaluated a multiplex assay that detects antibodies to three SARS-CoV-2 targets. Human serum specimens (n = 323) with known previous SARS-CoV-2 exposure status were tested on a commercially available multiplex bead assay (MBA) measuring IgG to SARS-CoV-2 spike protein receptor-binding domain (RBD), nucleocapsid protein (NP), and RBD/NP fusion antigens. Assay performance was evaluated against reverse transcriptase PCR (RT-PCR) results and also compared with test results for two single-target commercial assays. The MBA had a diagnostic sensitivity of 89.8% and a specificity of 100%, with serum collection at >28 days following COVID-19 symptom onset showing the highest seropositivity rates (sensitivity: 94.7%). The MBA performed comparably to single-target assays with the ability to detect IgG against specific antigen targets, with 19 (5.9%) discrepant specimens compared to the NP IgG assay and 12 (3.7%) compared to the S1 RBD IgG assay (kappa coefficients 0.92 and 0.88 compared to NP IgG and S1 RBD IgG assays, respectively. These findings highlight inherent advantages of using a SARS-CoV-2 serological test with multiple antigen targets; specifically, the ability to detect IgG against RBD and NP antigens simultaneously. In particular, the 100.0% diagnostic specificity exhibited by the MBA in this study is important for its implementation in populations with low SARS-CoV-2 seroprevalence or where background antibody reactivity to SARS-CoV-2 antigens has been detected.IMPORTANCE Reporting of SARS-CoV-2 infections through nucleic acid or antigen based diagnostic tests severely underestimates the true burden of exposure in a population. Serological data assaying for antibodies against SARS-CoV-2 antigens offers an alternative source of data to estimate population exposure, but most current immunoassays only include a single target for antibody detection. This report outlines a direct comparison of a multiplex bead assay to two other commercial single-target assays in their ability to detect IgG against SARS-CoV-2 antigens. Against a well-defined panel of 323 serum specimens, diagnostic sensitivity and specificity were very high for the multiplex assay, with strong agreement in IgG detection for single targets compared to the single-target assays. Collection of more data for individual- and population-level seroprofiles allows further investigation into more accurate exposure estimates and research into the determinants of infection and convalescent responses.

Seasonality of coronaviruses and other respiratory viruses in Canada: Implications for COVID-19

Background: Like endemic coronaviruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have emerged in humans from a zoonotic source and may ultimately develop a seasonal pattern. A seasonal pattern, particularly if combined with other seasonal outbreaks of respiratory virus infections, may have significant impacts on the healthcare system. We evaluated the seasonal pattern of existing endemic coronaviruses and several other common respiratory viruses to determine the potential impacts of added burden of respiratory disease should SARS-CoV-2 establish seasonality. Methods: National surveillance data for laboratory confirmations of endemic coronaviruses, influenza A and B viruses, rhinovirus/enterovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus for the past 10 years were obtained from the Government of Canada Open Data and FluWatch. Epidemic curves were generated from total case numbers and percent of samples testing positive for each respiratory virus by epidemiological week. Results: In Canada, endemic coronaviruses and other common respiratory viruses cause annual seasonal outbreaks in the winter months. Should SARS-CoV-2 develop a seasonal pattern similar to endemic coronaviruses and respiratory viruses, co-circulation would be expected to peak between January and March. Peak endemic coronavirus activity occurs during the nadir of rhinovirus/enterovirus and parainfluenza activity. Conclusion: Healthcare settings, assisted-living and long-term care homes, schools and essential services employers should anticipate and have contingencies for seasonal outbreaks of SARS-CoV-2 and co-circulating respiratory viruses during peak seasons. Given the likelihood of co-circulation, diagnostic multiplex testing targeting co-circulating pathogens may be more efficient than single target assays for symptomatic individuals if a seasonal pattern to coronavirus disease 2019 (COVID-19) is established.

Expression and processing of polycistronic artificial microRNAs and trans‐acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana

Targeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach; they have the advantage of producing just a single functional small RNA which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specialized trans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing in Solanum lycopersicum (tomato) and Nicotiana benthamiana. All analyses used transiently expressed expressed transgenes delivered by infiltration of leaves with Agrobacterium tumefacians. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5'-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3' end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time PCR, is also discussed.

A Highly Sensitive and Specific Gene Fusion Algorithm Based on Multiple Fusion Callers and an Ensemble Machine Learning Approach

Background: Gene Fusion events are common occurrences in malignancies, and are frequently drivers of malignancy. FISH and qPCR are two methods often used for identifying highly prevalent gene fusions/translocations. However, these are single target assays, requiring a lot of effort and sample if multiple assays are needed for multiple targets like sarcoma. High-throughput parallel (NextGen) DNA and RNA sequencing are also in current use to detect and characterize gene fusions. RNA sequencing (RNAseq) has the advantage that multiple markers can be targeted at one time and RNA fusions are readily identified from their product transcripts. While many fusion calling algorithms exist for use on RNAseq data, sensitive fusion callers, needed for samples of low tumor content, often present high false positive rates. Further, there currently is no single variable or element in NGS data that can be used to filter out false positive calls by extant callers. Individual sensitive fusion callers may be considered weak predictors of gene fusions. Combining their results into a single fusion call involves evaluating many elements, which can be a time consuming and difficult manual task. In order to achieve higher accuracy in fusion calls than can be achieved using individual fusion callers, we have combined the results of multiple fusion callers by use of an ensemble learning approach based on random forest models. Our method selects the best group of callers from among several callers, and provides an algorithmic means of combining their results, presenting a metric that can be immediately interpreted as the probability that a called fusion is a true fusion call. Methods: Random forest models were generated with the randomForest package in R, and then tuned using the R caret package. Training data sets consisted of fusion calls deemed true by review and by orthogonal methods including PCR/Sanger sequencing and the commercial Archer™ fusion calling system. We present the results of training on calls made by five fusion callers Arriba, STAR-Fusion, FusionCatcher, deFuse, and Kallisto/pizzly. Logistic training variables (seen vs not seen by the fusion caller) were used for the five callers. Variables also included metrics for the magnitude and balance of coverage on either side of candidate fusion breakpoints reported by Arriba and STAR Fusion ("coverage balance") and a single metric consisting of the number of sequencing reads that cross the candidate breakpoint. The model was validated by 10-fold cross-validation on 598 fusion calls by the five callers. Results: The resulting model is superior to the simple strategy of requiring agreement by n of five callers, particularly with regard to specificity (Table 1). Also, "importance of variables," reported by randomForest, gauges the relative contribution of variables in the model. Here it shows that one caller, Kallisto\pizzly, does not contribute to the model (Table 2). Conclusion: Random Forest modeling provides a viable means of combining gene fusion call data from multiple callers into a single fusion calling tool with improved performance over simple combinations of fusion calls. An additional benefit is seen in that building and evaluating such models can guide the selection of fusion callers, thereby eliminating non-contributory calling methods and ensuring optimal utilization of computational resources. Disclosures Thomas: NeoGenomics,Inc.: Current Employment. Mou:NeoGenomics: Current Employment. Keeler:NeoGenomics: Current Employment. Magnan:NeoGenomics: Current Employment. Funari:NeoGenomics: Current Employment. Weiss:Merck: Other: Speaker; Bayer: Other: speaker; Genentech: Other: Speaker; NeoGenomics: Current Employment. Brown:NeoGenomics,Inc.: Current Employment. Agersborg:NeoGenomics: Current Employment.

Development and Clinical Validation of Discriminatory Multitarget Digital Droplet PCR Assays for the Detection of Hot Spot KRAS and NRAS Mutations in Cell-Free DNA

Detection and quantification of tumor-derived KRAS and NRAS mutations in plasma cell-free DNA (cfDNA) holds great potential for cancer diagnostics and treatment response monitoring. Because of high sensitivity, specificity, robustness, and affordability, digital droplet PCR (ddPCR) is ideally suited for this application but requires discriminatory multiplexing when used as screening assay. We therefore designed, optimized, and clinically validated mutation-specific locked nucleic acid-based ddPCR assays for 14 commonly occurring KRAS and NRAS mutations and assembled these assays into seven discriminatory multitarget screening assays covering two to six single-nucleotide variants each. Limit of detection, limit of blank, and interassay accuracy were determined. Assay performance and suitability for screening in cfDNA were validated with plasma samples from a clinically fully characterized cohort of pancreatic cancer patients and healthy controls. Limits of detection for single-target assays were between 0.0015% and 0.069% variant allele fraction, and between 0.022% and 0.16% for multitarget assays. Dilution linearity and interassay accuracy were excellent throughout (r2>0.99). Multitarget assay screening of cfDNA extracted from pancreatic cancer patients with unknown KRAS mutational status correctly identified single-nucleotide variants in 45 of 45 (100%) of tumor-derived cell-free DNA-positive samples. In summary, we herein present and clinically validate generic single-target and discriminatory multitarget ddPCR assays for KRAS and NRAS hot spot mutations with broad applicability for clinical and translational research.

Hazard Characterization of Synthetic Cathinones Using Viability, Monoamine Reuptake, and Neuronal Activity Assays.

Synthetic cathinones are the second largest class of new psychoactive substances (NPS) on the drug market. Despite the large number of different cathinones and their abundant use, hazard characterization is mainly limited to their potential to inhibit monoamine transporters. To expand the current hazard characterization, we first investigated the acute effects of several synthetic cathinones [4-methylethcathinone (4-MEC), 3-methylmethcathinone (3-MMC), 4-MMC, methylone, pentedrone, α-pyrrolidinovalerophenone (α-PVP), and 3,4-methylenedioxypyrovalerone (MDPV)] on human dopamine, norepinephrine, and serotonin reuptake transporters (hDAT, hNET, and hSERT), which were stably transfected in human embryonic kidney (HEK) 293 cells. Next, we examined effects on spontaneous neuronal activity in rat primary cortical cultures grown on microelectrode arrays (MEAs) as an integrated endpoint for neurotoxicity. Changes in neuronal activity were assessed after acute (30 min) and prolonged (4.5 h) exposure. Moreover, we investigated whether neuronal activity recovered after washout of the exposure (24 h after the start of the 5 h exposure). Low micromolar concentrations of synthetic cathinones inhibited monoamine uptake via hDAT and hNET, while higher cathinone concentrations were needed to inhibit uptake via hSERT. Comparable high concentrations were needed to inhibit spontaneous neuronal activity during acute (30 min) and prolonged (4.5 h) exposure. Notably, while the inhibition of neuronal activity was reversible at low concentrations, only partial recovery was seen following high, but non-cytotoxic, concentrations of synthetic cathinones. Synthetic cathinones with either a pyrrolidine moiety or long alkyl-tail carbon chain more potently inhibit monoamine uptake via hDAT and neuronal activity. Monoamine uptake via hNET was most potently inhibited by synthetic cathinones with a pyrrolidine moiety. The combination of integrated measurements (MEA recordings of neuronal activity) with single target assays (monoamine reuptake transporter inhibition) indicates inhibition of hDAT and hNET as the primary mode of action of these synthetic cathinones. Changes in neuronal activity, indicative for additional mechanisms, were observed at higher concentrations.

Simultaneous detection of multiple pathogens by multiplex PCR coupled with DNA biochip hybridization.

Traditional serological enzyme-linked immunosorbent assay (ELISA) is routinely used to monitor pathogens during quarantine in most animal facilities to prevent possible infection. However, the ELISA platform is a single-target assay, and screening all targeted pathogens is time-consuming and laborious. In this study, to increase sensitivity and to reduce diagnosis time for high-throughput processes, multiplex PCR and DNA biochip techniques were combined to develop a multi-pathogen diagnostic method for use instead of routine ELISA. Eight primer sets were designed for multiplex PCR to detect genes from seven targeted bacterial and viral pathogens. DNA-DNA hybridization was conducted on a biochip following the multiple PCR analysis. Using this method, a total of 24 clinical samples were tested, and the result showed that not only single infection but also co-infection by multi-pathogens can be detected. In conclusion, multiplex PCR coupled with a DNA biochip is an efficient method for detecting multi-pathogens in a reaction. This platform is a useful tool for quarantine services and disease prevention in animal facilities.

Development and evaluation of an up-converting phosphor technology-based lateral flow assay for the rapid, simultaneous detection of Vibrio cholerae serogroups O1 and O139.

Vibrio cholerae serogroups O1 and O139 are etiological agents of cholera, a serious and acute diarrheal disease, and rapid detection of V. cholerae is a key method for preventing and controlling cholera epidemics. Here, a point of care testing (POCT) method called Vch-UPT-LF, which is an up-converting phosphor technology-based lateral flow (UPT-LF) assay with a dual-target detection mode, was developed to detect V. cholerae O1 and O139 simultaneously from one sample loading. Although applying an independent reaction pair made both detection results for the two Vch-UPT-LF detection channels more stable, the sensitivity slightly declined from 104 to 105 colony-forming units (CFU) mL−1 compared with that of the single-target assay, while the quantification ranges covering four orders of magnitude were maintained. The strip showed excellent specificity for seven Vibrio species that are highly related genetically, and nine food-borne species whose transmission routes are similar to those of V. cholerae. The legitimate arrangement of the two adjacent test lines lessened the mutual impact of the quantitation results between the two targets, and the quantification values did not differ by more than one order of magnitude when the samples contained high concentrations of both V. cholerae O1 and O139. Under pre-incubation conditions, 1×101 CFU mL−1 of V. cholerae O1 or O139 could be detected in fewer than 7 h, while the Vch-UPT-LF assay exhibited sensitivity as high as a real-time fluorescent polymerase chain reaction with fewer false-positive results. Therefore, successful development of Vch-UPT-LF as a dual-target assay for quantitative detection makes this assay a good candidate POCT method for the detection and surveillance of epidemic cholera.

Colorimetric aptasensor using unmodified gold nanoparticles for homogeneous multiplex detection.

Colorimetric aptasensors using unmodified gold nanoparticles (AuNPs) have attracted much attention because of their low cost, simplicity, and practicality, and they have been developed for various targets in the past several years. However, previous research has focused on developing single-target assays. Here, we report the development of a homogeneous multiplex aptasensor by using more than one class of aptamers to stabilize AuNPs. Using sulfadimethoxine (SDM), kanamycin (KAN) and adenosine (ADE) as example targets, a KAN aptamer (750 nM), an SDM aptamer (250 nM) and an ADE aptamer (500 nM) were mixed at a 1∶1∶1 volume ratio and adsorbed directly onto the surface of unmodified AuNPs by electrostatic interaction. Upon the addition of any of the three targets, the conformation of the corresponding aptamer changed from a random coil structure to a rigid folded structure, which could not adsorb and stabilize AuNPs. The AuNPs aggregated in a specific reaction buffer (20 mM Tris-HCl containing 20 mM NaCl and 5 mM KCl), which led to a color change from red to purple/blue. These results demonstrate that the multiplex colorimetric aptasensor detected three targets simultaneously while maintaining the same sensitivity as a single-target aptasensor for each individual target. The multiplex aptasensor could be extended to other aptamers for various molecular detection events. Due to its simple design, easy operation, fast response, cost effectiveness and lack of need for sophisticated instrumentation, the proposed strategy provides a powerful tool to examine large numbers of samples to screen for a small number of potentially positive samples containing more than one analyte, which can be further validated using sophisticated instruments.

MNAzyme qPCR with Superior Multiplexing Capacity

MNAzymes (nucleic acid enzymes formed from multiple partial enzymes) can be linked to PCR to provide a highly specific method for target detection and quantification. We investigated the feasibility of multiplexing MNAzyme quantitative PCR (qPCR) methods. We combined MNAzyme components with PCR primers and standard qPCR reagents to perform MNAzyme qPCR and reverse-transcription qPCR (RT-qPCR) assays with a set of universal reporter probes. Assays were performed on single targets and in multiplex formats that combined up to 5 different targets in a single reaction. A comparison of 3 targets amplified in single and triplex formats showed no significant differences with respect to detection limit or amplification efficiency. Likewise, we successfully converted single-target assays for 11 transcripts of interest to triplex assays containing 2 reference transcripts without having to optimize or modify the conditions. A quintuplex RT-qPCR that simultaneously quantified 5 transcripts with 5 universal probes produced high amplification efficiencies and r(2) values for all transcripts. Despite the large numbers of oligonucleotides in the reactions, we observed no false-positive signals, owing to the requirement of 4 target-specific binding events to produce a signal. A quadruplex assay that combined MNAzymes with methylation-specific PCR to measure epigenetic biomarkers of prostate cancer was capable of detecting a single methylated DNA allele in a background of 1000-10 000 unmethylated alleles. The MNAzyme qPCR was compatible with a rapid-cycling protocol. MNAzymes offer a flexible and unique approach to qPCR that is specific, sensitive, and easily multiplexed. The universal nature of MNAzyme reporter probes removes the need for target-specific probes, thereby making the development of new assays easier and cheaper.

Multiplex Detection of DNA Sequences Using the Volume-Amplified Magnetic Nanobead Detection Assay

The possibility for conducting multiplex detection of DNA-sequences using the volume-amplified magnetic nanobead detection assay [Stromberg, M.; Goransson, J.; Gunnarsson, K.; Nilsson, M.; Svedlindh, P. and Strømme, M. Nano Lett. 2008 , 8, 816-821] was investigated. In this methodology, a batch consisting of a mixture of several sizes of probe-tagged magnetic beads was used for detection of several types of targets in the same compartment. Furthermore, a nonlinear least-squares deconvolution procedure of the composite imaginary part of complex magnetization vs frequency spectra based on the Cole-Cole model was applied to analyze the data. The results of a quantitative biplex analysis experiment were compared with the corresponding separate single-target assays. Finally, triplex analysis was briefly demonstrated qualitatively. Biplex and triplex detection were found to perform well qualitatively. Biplex detection was found to enable a rough target quantification. Multiplex detection may become a complement to performing multiple separate single-target assays for, e.g., parallel detection of multiple infectious pathogens. Multiplex detection also permits robust relative quantification and inclusion of an internal control to improve quantification accuracy.

Duplex-PCR assay for the detection of adenovirus and respiratory syncytial virus in nasopharyngeal samples

Human adenovirus (HAdV) and human respiratory syncytial virus (HRSV) are important etiologic agents of acute respiratory infections. In this study, a duplex polymerase chain reaction (PCR) assay was developed for the simultaneous detection of HAdV and HRSV in clinical samples. Sixty previously screened nasopharyngeal aspirates were used: 20 HAdV-positive, 20 HRSV-positive and 20 double-negative controls. Eight samples were positive for both viruses. The duplex PCR assay proved to be as sensitive and specific as single-target assays and also detected the mixed infections with certainty. The identification of both viruses in a single reaction offers a reduction in both cost and laboratory diagnostic time.