scholarly journals A Portable Device for LAMP Based Detection of SARS-CoV-2

Micromachines ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1151
Author(s):  
Kamalalayam Rajan Sreejith ◽  
Muhammad Umer ◽  
Larissa Dirr ◽  
Benjamin Bailly ◽  
Patrice Guillon ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Copy Number ◽  
Low Cost ◽  
Quantitative Polymerase Chain Reaction ◽  
Portable Device ◽  
Design Development ◽  
Isothermal Heating ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Template Copy

This paper reports the design, development, and testing of a novel, yet simple and low-cost portable device for the rapid detection of SARS-CoV-2. The device performs loop mediated isothermal amplification (LAMP) and provides visually distinguishable images of the fluorescence emitted from the samples. The device utilises an aluminium block embedded with a cartridge heater for isothermal heating of the sample and a single-board computer and camera for fluorescence detection. The device demonstrates promising results within 20 min using clinically relevant starting concentrations of the synthetic template. Time-to-signal data for this device are considerably lower compared to standard quantitative Polymerase Chain Reaction(qPCR) machine (~10–20 min vs. >38 min) for 1 × 102 starting template copy number. The device in its fully optimized and characterized state can potentially be used as simple to operate, rapid, sensitive, and inexpensive platform for population screening as well as point-of-need severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) detection and patient management.

scholarly journals A Portable Device for LAMP Based Detection of Sars-Cov-2

2021 ◽  
Author(s):  
Kamalalayam Rajan Sreejith ◽  
Muhammad Umer ◽  
Narshone Soda ◽  
Surasak Kasetsirikul ◽  
Muhammad Shiddiky ◽  
...  
Keyword(s):  
Fluorescence Detection ◽  
Rapid Detection ◽  
Copy Number ◽  
Patient Management ◽  
Low Cost ◽  
Portable Device ◽  
Design Development ◽  
Isothermal Heating ◽  
Template Copy ◽  
Cartridge Heater

This paper reports the design, development, and testing of a novel, yet simple and low-cost portable device for the rapid detection of SARS-CoV-2. The device performs loop mediated isothermal amplification (LAMP) and provides visually distinguishable images of the fluorescence emitted from the samples. The device utilises an aluminium block embedded with a cartridge heater for isothermal heating of the sample and a single-board computer and camera for fluorescence detection. The device demonstrates promising results within 20 minutes using clinically relevant starting concentrations of the synthetic template. Time-to-signal data for this device are considerably lower compared to standard qPCR machine (~10-20 minutes vs >38 minutes) for 1×105 starting template copy number. The device in its fully optimized and characterized state can potentially be used as simple to operate, rapid, sensitive, and inexpensive platform for population screening as well as point-of-need SARS-CoV-2 detection and patient management.

Relationship Between MYCN Copy Number and Expression in Rhabdomyosarcomas and Correlation With Adverse Prognosis in the Alveolar Subtype

2005 ◽  
Vol 23 (4) ◽  
pp. 880-888 ◽  
Author(s):  
Daniel Williamson ◽  
Yong-Jie Lu ◽  
Tony Gordon ◽  
Raf Sciot ◽  
Anna Kelsey ◽  
...  
Keyword(s):  
Pediatric Cancer ◽  
Copy Number ◽  
Adverse Outcome ◽  
Quantitative Polymerase Chain Reaction ◽  
High Copy Number ◽  
Molecular Diagnostic ◽  
Chain Reaction ◽  
Clinicopathologic Characteristics ◽  
Expression Levels ◽  
Polymerase Chain

Purpose Amplification of the transcription factor MYCN is an important molecular diagnostic tool in stratifying treatment for neuroblastoma. Increased copy number and overexpression of MYCN in the pediatric cancer rhabdomyosarcoma has been described in a number of small studies with conflicting conclusions about its association with clinicopathologic characteristics. We aimed to study the phenomenon in the largest series to date. Patients and Methods Using quantitative polymerase chain reaction, we measured MYCN copy number and expression levels in rhabdomyosarcoma samples from 113 and 92 individuals with a confirmed diagnosis of rhabdomyosarcoma, respectively. Results Increased copy number of MYCN was found to be a feature of both the embryonal and alveolar subtypes. The copy number and expression levels were significantly greater in the alveolar subtype, although the range of expression in both subtypes spanned several orders of magnitude. MYCN copy number showed a significant correlation with expression in the alveolar subtype; this relationship between copy number and expression could be modeled as a logarithmic function. It is notable that relatively high expression frequently occurred in embryonal rhabdomyosarcoma without high copy number and that low expression was found in some cases with high copy number. In patients with alveolar rhabdomyosarcoma, overexpression (greater than median) or gain of genomic copies of MYCN were significantly associated with adverse outcome. Conclusion MYCN deregulation is a feature of rhabdomyosarcoma tumorigenesis, defines groups of patients with a poor prognosis, and is a potential target for novel therapies.

scholarly journals Evaluation method for asymmetric uncertainty of quantitative polymerase chain reaction measurements of deoxyribonucleic acids with low copy number

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Unoh Ki ◽  
Takeru Suzuki ◽  
Satoshi Nakazawa ◽  
Yuuki Yonekawa ◽  
Kazuki Watanabe ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Confidence Interval ◽  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Limit Of Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Low Copy Number ◽  
Polymerase Chain

AbstractRecently, in food safety and various other fields, qualitative and quantitative gene analysis using real-time polymerase chain reaction (PCR) method has become increasingly popular. The limit of detection (LOD) and quantifiable range for these measurements depends on the range and precision of DNA calibrators’ concentrations. Low-copy-number nucleic acid reference materials with low uncertainty produced by an inkjet system have been developed to allow for precise measurements in a low-copy-number region. However, when using a calibrator with a low copy number near one, the copy number distribution is asymmetric. Consequently, the confidence intervals of estimated copy numbers can include negative values when conventional methods of uncertainty estimation are used. A negative confidence interval is irrelevant in the context of copy number, which is always positive value or zero. Here, we propose a method to evaluate the uncertainty of real-time PCR measurements with representative values and an asymmetric 95% confidence interval. Moreover, we use the proposed method for the actual calculation of uncertainty of real-time PCR measurement results for low-copy-number DNA samples and demonstrate that the proposed method can evaluate the precision of real-time PCR measurements more appropriately in a low-copy-number region.

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