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Journal of Clinical Oncology : Official... Dec 2017Standard methods for disease response assessment in patients with lymphoma, including positron emission tomography and computed tomography scans, are imperfect. In other... (Review)
Review
Standard methods for disease response assessment in patients with lymphoma, including positron emission tomography and computed tomography scans, are imperfect. In other hematologic malignancies, particularly leukemias, the ability to detect minimal residual disease (MRD) is increasingly influencing treatment paradigms. However, in many subtypes of lymphoma, the application of MRD assessment techniques, like flow cytometry or polymerase chain reaction-based methods, has been challenging because of the absence of readily detected circulating disease or canonic chromosomal translocations. Newer MRD detection methods that use next-generation sequencing have yielded promising results in a number of lymphoma subtypes, fueling the hope that MRD detection may soon be applicable in clinical practice for most patients with lymphoma. MRD assessment can provide real-time information about tumor burden and response to therapy, noninvasive genomic profiling, and monitoring of clonal dynamics, allowing for many possible applications that could significantly affect the care of patients with lymphoma. Further validation of MRD assessment methods, including the incorporation of MRD assessment into clinical trials in patients with lymphoma, will be critical to determine how best to deploy MRD testing in routine practice and whether MRD assessment can ultimately bring us closer to the goal of personalized lymphoma care. In this review article, we describe the methods available for detecting MRD in patients with lymphoma and their relative advantages and disadvantages. We discuss preliminary results supporting the potential applications for MRD testing in the care of patients with lymphoma and strategies for including MRD assessment in lymphoma clinical trials.
Topics: Female; Flow Cytometry; Humans; Lymphoma; Male; Neoplasm, Residual; Polymerase Chain Reaction; Randomized Controlled Trials as Topic; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Sensitivity and Specificity
PubMed: 28933999
DOI: 10.1200/JCO.2017.74.5281 -
Medecine Sciences : M/S Feb 2018After years of development, the use of nanopore as a sensor to sequence DNA molecules is now a viable and promising possibility. Single base pair detection during DNA... (Review)
Review
After years of development, the use of nanopore as a sensor to sequence DNA molecules is now a viable and promising possibility. Single base pair detection during DNA transport enables to record ultra-long threads with high parallelization and rates. I will present in this review the current methodologies based on electrical detection and biological nanopores and the new methods based on solid state nanopores and optical detection.
Topics: Action Potentials; Animals; Commerce; Electric Conductivity; High-Throughput Nucleotide Sequencing; Humans; Nanopores; Nanotechnology; Polymerase Chain Reaction; Sequence Analysis, DNA
PubMed: 29451487
DOI: 10.1051/medsci/20183402014 -
SLAS Technology Oct 2022Thermal cyclers are used to perform polymerase chain reaction runs (PCR runs) and Peltier modules are the key components in these instruments. The demand for thermal...
Thermal cyclers are used to perform polymerase chain reaction runs (PCR runs) and Peltier modules are the key components in these instruments. The demand for thermal cyclers has strongly increased during the COVID-19 pandemic due to the fact that they are important tools used in the research, identification, and diagnosis of the virus. Even though Peltier modules are quite durable, their failure poses a serious threat to the integrity of the instrument, which can lead to plant shutdowns and sample loss. Therefore, it is highly desirable to be able to predict the state of health of Peltier modules and thus reduce downtime. In this paper methods from three sub-categories of supervised machine learning, namely classical methods, ensemble methods and convolutional neural networks, were compared with respect to their ability to detect the state of health of Peltier modules integrated in thermal cyclers. Device-specific data from on-deck thermal cyclers (ODTC®) supplied by INHECO Industrial Heating & Cooling GmbH (Fig 1), Martinsried, Germany were used as a database for training the models. The purpose of this study was to investigate methods for data-driven condition monitoring with the aim of integrating predictive analytics into future product platforms. The results show that information about the state of health can be extracted from operational data - most importantly current readings - and that convolutional neural networks were the best at producing a generalized model for fault classification.
Topics: COVID-19; Humans; Machine Learning; Neural Networks, Computer; Pandemics; Polymerase Chain Reaction
PubMed: 35908645
DOI: 10.1016/j.slast.2022.07.002 -
Analytical Chemistry Jan 2017Polymerase chain reaction (PCR) is dependent on two key hybridization events during each cycle of amplification, primer annealing and product melting. To ensure that...
Polymerase chain reaction (PCR) is dependent on two key hybridization events during each cycle of amplification, primer annealing and product melting. To ensure that these hybridization events occur, current PCR approaches rely on temperature set points and reaction contents that are optimized and maintained using rigid thermal cycling programs and stringent sample preparation procedures. This report describes a fundamentally simpler and more robust PCR design that dynamically controls thermal cycling by more directly monitoring the two key hybridization events during the reaction. This is achieved by optically sensing the annealing and melting of mirror-image l-DNA analogs of the reaction's primers and targets. Because the properties of l-DNA enantiomers parallel those of natural d-DNAs, the l-DNA reagents indicate the cycling conditions required for effective primer annealing and product melting during each cycle without interfering with the reaction. This hybridization-sensing approach adapts in real time to variations in reaction contents and conditions that impact primer annealing and product melting and eliminates the requirement for thermal calibrations and cycling programs. Adaptive PCR is demonstrated to amplify DNA targets with high efficiency and specificity under both controlled conditions and conditions that are known to cause traditional PCR to fail. The advantages of this approach promise to make PCR-based nucleic acid analysis simpler, more robust, and more accessible outside of well-controlled laboratory settings.
Topics: DNA; DNA Probes; Polymerase Chain Reaction; Temperature
PubMed: 28105843
DOI: 10.1021/acs.analchem.6b03291 -
International Journal of Molecular... May 2019New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on... (Review)
Review
New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on digital polymerase chain reaction (PCR). Digital PCR (dPCR) is a breakthrough technology designed to provide absolute nucleic acid quantification. It is particularly useful to detect a low amount of target and therefore it represents an alternative method for detecting measurable residual disease (MRD). The main advantages are the high precision, the very reliable quantification, the absolute quantification without the need for a standard curve, and the excellent reproducibility. Nowadays the main disadvantages of this strategy are the costs that are still higher than standard qPCR, the lack of standardized methods, and the limited number of laboratories that are equipped with instruments for dPCR. Several studies describing the possibility and advantages of using digital PCR for the detection of specific leukemic transcripts or mutations have already been published. In this review we summarize the available data on the use of dPCR in acute myeloid leukemia and myeloproliferative disorders.
Topics: Biomarkers, Tumor; Humans; Leukemia, Myeloid, Acute; Molecular Diagnostic Techniques; Polymerase Chain Reaction
PubMed: 31067725
DOI: 10.3390/ijms20092249 -
Biosensors Feb 2023Recently, infectious diseases, such as COVID-19, monkeypox, and Ebola, are plaguing human beings. Rapid and accurate diagnosis methods are required to preclude the...
Recently, infectious diseases, such as COVID-19, monkeypox, and Ebola, are plaguing human beings. Rapid and accurate diagnosis methods are required to preclude the spread of diseases. In this paper, an ultrafast polymerase chain reaction (PCR) equipment is designed to detect virus. The equipment consists of a silicon-based PCR chip, a thermocycling module, an optical detection module, and a control module. Silicon-based chip, with its thermal and fluid design, is used to improve detection efficiency. A thermoelectric cooler (TEC), together with a computer-controlled proportional-integral-derivative (PID) controller, is applied to accelerate the thermal cycle. A maximum of four samples can be tested simultaneously on the chip. Two kinds of fluorescent molecules can be detected by optical detection module. The equipment can detect viruses with 40 PCR amplification cycles in 5 min. The equipment is portable, easily operated, and low equipment cost, which shows great potential in epidemic prevention.
Topics: Humans; Silicon; Microfluidics; COVID-19; Polymerase Chain Reaction; Viruses; Nucleic Acids; Nucleic Acid Amplification Techniques; Microfluidic Analytical Techniques; Equipment Design
PubMed: 36832000
DOI: 10.3390/bios13020234 -
Expert Review of Molecular Diagnostics 2016The remarkable stability of microRNAs in biofluids underlies their potential as biomarkers, but their small size presents challenges for detection by RT-qPCR. The... (Review)
Review
The remarkable stability of microRNAs in biofluids underlies their potential as biomarkers, but their small size presents challenges for detection by RT-qPCR. The heterogeneity of microRNAs, with each one comprising a series of variants or 'isomiRs', adds additional complexity. Presented here are the key considerations for use of RT-qPCR to measure microRNAs and their isomiRs, with a focus on plasma. Modified nucleotides can be incorporated into primer sequences to enhance affinity and provide increased specificity and sensitivity for RT-qPCR assays. Approaches based upon polyA tailing and use of a common oligo(dT)-based reverse transcription oligonucleotide will detect most isomiRs. Conversely, stem-loop RT oligonucleotides and sequence specific probes can enable detection of specific isomiRs of interest. Next generation sequencing of all the products of a microRNA RT-PCR reaction is a promising new approach for both microRNA quantification and characterization.
Topics: Biomarkers; Humans; MicroRNAs; Molecular Diagnostic Techniques; Polymerase Chain Reaction; Sequence Analysis, RNA
PubMed: 26854938
DOI: 10.1586/14737159.2016.1152184 -
Nucleic Acids Research Jul 2019Quality control (QC) for lab-designed primers is crucial for the success of a polymerase chain reaction (PCR). Here, we present MFEprimer-3.0, a functional primer...
Quality control (QC) for lab-designed primers is crucial for the success of a polymerase chain reaction (PCR). Here, we present MFEprimer-3.0, a functional primer quality control program for checking non-specific amplicons, dimers, hairpins and other parameters. The new features of the current version include: (i) more sensitive binding site search using the updated k-mer algorithm that allows mismatches within the k-mer, except for the first base at the 3' end. The binding sites of each primer with a stable 3' end are listed in the output; (ii) new algorithms for rapidly identifying self-dimers, cross-dimers and hairpins; (iii) the command-line version, which has an added option of JSON output to enhance the versatility of MFEprimer by acting as a QC step in the 'primer design → quality control → redesign' pipeline; (iv) a function for checking whether the binding sites contain single nucleotide polymorphisms (SNPs), which will affect the consistency of binding efficiency among different samples. In summary, MFEprimer-3.0 is updated with the well-tested PCR primer QC program and it can be integrated into various PCR primer design applications as a QC module. The MFEprimer-3.0 server is freely accessible without any login requirement at: https://mfeprimer3.igenetech.com/ and https://www.mfeprimer.com/. The source code for the command-line version is available upon request.
Topics: Algorithms; Base Pair Mismatch; Binding Sites; DNA Primers; Genome, Human; Humans; Multiplex Polymerase Chain Reaction; Polymerase Chain Reaction; Quality Control; Sequence Analysis; Software
PubMed: 31066442
DOI: 10.1093/nar/gkz351 -
Molecular Diagnosis & Therapy Jun 2017Circulating RNAs, especially microRNAs (miRNAs), have recently emerged as non-invasive disease biomarkers. Despite enthusiasm and numerous reports on disease-associated... (Review)
Review
Circulating RNAs, especially microRNAs (miRNAs), have recently emerged as non-invasive disease biomarkers. Despite enthusiasm and numerous reports on disease-associated circulating miRNAs, currently there is no circulating miRNA-based diagnostic in use. In addition, there are many contradictory reports on the concentration changes of specific miRNA in circulation. Here we review the impact of various technical and non-technical factors related to circulating miRNA measurement and elucidate the importance of having a general guideline for sample preparation and concentration measurement in studying circulating RNA.
Topics: Biomarkers, Tumor; Blood Platelets; Cell-Free Nucleic Acids; Diet; Exercise; Female; Genetic Markers; High-Throughput Nucleotide Sequencing; Humans; Male; MicroRNAs; Polymerase Chain Reaction; Specimen Handling; Time Factors
PubMed: 28039578
DOI: 10.1007/s40291-016-0251-y -
American Journal of Infection Control Oct 2015Efforts to reduce health care-associated infections (HAIs) have grown in both scale and sophistication over the past few decades; however, the increasing threat of...
Efforts to reduce health care-associated infections (HAIs) have grown in both scale and sophistication over the past few decades; however, the increasing threat of antimicrobial resistance and the impact of new legislation regarding HAIs on health care economics make the fight against them all the more urgent. On-demand polymerase chain reaction (PCR) technology has proven to be a highly effective weapon in this fight, offering the ability to accurately and efficiently identify disease-causing pathogens such that targeted and directed therapy can be initiated at the point of care. As a result, on-demand PCR technology has far-reaching influences on HAI rates, health care outcomes, hospital length of stay, isolation days, patient satisfaction, antibiotic stewardship, and health care economics. The basics of on-demand PCR technology and its potential to impact health care have not been widely incorporated into health care education and enrichment programs for many of those involved in infection control and prevention, however. This article serves as a primer on on-demand PCR technology and its ramifications.
Topics: Cross Infection; Humans; Molecular Diagnostic Techniques; Point-of-Care Testing; Polymerase Chain Reaction
PubMed: 26198577
DOI: 10.1016/j.ajic.2015.06.001