Data-driven normalization strategies for high-throughput quantitative RT-PCR

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

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Improved real-time RT-PCR method for high-throughput measurements using second derivative calculation and double correction

BioTechniques ◽

10.2144/05382rr05 ◽

2005 ◽

Vol 38 (2) ◽

pp. 287-293 ◽

Cited By ~ 183

Author(s):

Van Luu-The ◽

Nathalie Paquet ◽

Ezequiel Calvo ◽

Jean Cumps

Keyword(s):

Real Time ◽

High Throughput ◽

Second Derivative ◽

Rt Pcr ◽

Pcr Method

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Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre

Journal of Chemical Information and Modeling ◽

10.1021/ci2002523 ◽

2011 ◽

Vol 51 (11) ◽

pp. 2787-2787 ◽

Cited By ~ 5

Author(s):

Colin R Groom

Keyword(s):

Small Molecules ◽

High Throughput ◽

Crystallographic Data ◽

Data Driven ◽

Cambridge Crystallographic Data Centre ◽

Data Centre

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Comparison of high throughput sequencing to standard protocols for virus detection in berry crops

Plant Disease ◽

10.1094/pdis-05-21-0949-re ◽

2021 ◽

Author(s):

Dan Edward Veloso Villamor ◽

Karen E Keller ◽

Robert Martin ◽

Ioannis Emmanouil Tzanetakis

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Wide Spectrum ◽

Virus Detection ◽

Rt Pcr ◽

Host Interactions ◽

Growing Seasons ◽

Berry Crops ◽

Sampling Times ◽

Better Than

A comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium and 8 Rubus) with known virus profiles was completed. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, RT-PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared to RT-PCR on a wide spectrum of virus variants and discovery of novel viruses. More importantly, in most cases where the two protocols showed parallel virus detection, 11 viruses in 16 berry selections were not consistently detected by both methods at all sampling points. Based on these data we propose a four sampling times/two-year testing requirement for berry and potentially other crops to ensure that no virus remains undetected independent of titer, distribution or other virus/virus or virus/host interactions.

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Multiplex Detection of Rotavirus A, B, C, Norovirus GI and GII, Adenovirus, Astrovirus and Sapovirus in a Single PCR System in Stool Samples From Acute Diarrhea Children

10.21203/rs.3.rs-111216/v1 ◽

2020 ◽

Author(s):

Wei Li ◽

Weiwei Li ◽

Ran Tao ◽

Wenqing Xiang ◽

Mingming Zhou ◽

...

Keyword(s):

High Throughput ◽

Acute Diarrhea ◽

Cross Reaction ◽

Melting Curve Analysis ◽

Clinical Test ◽

Rt Pcr ◽

Rotavirus A ◽

Diarrhea Virus ◽

Intestinal Pathogens ◽

Stool Samples

Abstract Background: Early and accurate identification of infection viruses among children can benefit the personalized medical treatment and management, and reduce the future occurrence of serious symptoms. Thus, it is critical to develop a high-throughput multiplex real-time RT-PCR method to improve the accuracy and efficiency in routine clinical lab tests. Here, we developed a RT-PCR combined with melting curve analysis (RRCMC) method for simultaneous detection of rotavirus A, B, C, norovirus GI and GII, adenovirus, astrovirus and sapovirus. Results: Stool samples were collected from 160 children with acute diarrhea and tested by RRCMC assay. A total of 71 patients were tested positive with norovirus, adenovirus or rotavirus. The RRCMC assay has high specificity. There is no internal cross-reaction through the 8 diarrhea viruses and no cross-reaction of other commonly intestinal pathogens and human genome. The detection limit was ranging from 1×102 to 1×105 copies/ml for each diarrhea virus. Conclusions: In conclusion, the RRCMC method is a suitable rapid clinical test for infection viruses, with the advantages of high-throughput, low cost, high sensitivity, and specificity.

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Expression profile of microRNAs in gastrointestinal stromal tumors revealed by high throughput quantitative RT-PCR microarray

World Journal of Gastroenterology ◽

10.3748/wjg.v21.i19.5843 ◽

2015 ◽

Vol 21 (19) ◽

pp. 5843-5855 ◽

Cited By ~ 13

Author(s):

Han-Xing Tong ◽

Yu-Hong Zhou ◽

Ying-Yong Hou ◽

Yong Zhang ◽

Yuan Huang ◽

...

Keyword(s):

Expression Profile ◽

High Throughput ◽

Gastrointestinal Stromal Tumors ◽

Rt Pcr ◽

Stromal Tumors ◽

Pcr Microarray

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ChemSpaX: Exploration of Chemical Space by Automated Functionalization of Molecular Scaffold

10.26434/chemrxiv.14617320 ◽

2021 ◽

Author(s):

Adarsh Kalikadien ◽

Evgeny A. Pidko ◽

Vivek Sinha

Keyword(s):

Force Field ◽

High Throughput ◽

High Throughput Screening ◽

Chemical Space ◽

Space Exploration ◽

Molecular Structures ◽

Data Driven ◽

Pincer Complexes ◽

Cobalt Porphyrin ◽

Input Structure

<div>Local chemical space exploration of an experimentally synthesized material can be done by making slight structural</div><div>variations of the synthesized material. This generation of many molecular structures with reasonable quality,</div><div>that resemble an existing (chemical) purposeful material, is needed for high-throughput screening purposes in</div><div>material design. Large databases of geometry and chemical properties of transition metal complexes are not</div><div>readily available, although these complexes are widely used in homogeneous catalysis. A Python-based workflow,</div><div>ChemSpaX, that is aimed at automating local chemical space exploration for any type of molecule, is introduced.</div><div>The overall computational workflow of ChemSpaX is explained in more detail. ChemSpaX uses 3D information,</div><div>to place functional groups on an input structure. For example, the input structure can be a catalyst for which one</div><div>wants to use high-throughput screening to investigate if the catalytic activity can be improved. The newly placed</div><div>substituents are optimized using a computationally cheap force-field optimization method. After placement of</div><div>new substituents, higher level optimizations using xTB or DFT instead of force-field optimization are also possible</div><div>in the current workflow. In representative applications of ChemSpaX, it is shown that the structures generated by</div><div>ChemSpaX have a reasonable quality for usage in high-throughput screening applications. Representative applications</div><div>of ChemSpaX are shown by investigating various adducts on functionalized Mn-based pincer complexes,</div><div>hydrogenation of Ru-based pincer complexes, functionalization of cobalt porphyrin complexes and functionalization</div><div>of a bipyridyl functionalized cobalt-porphyrin trapped in a M2L4 type cage complex. Descriptors such as</div><div>the Gibbs free energy of reaction and HOMO-LUMO gap, that can be used in data-driven design and discovery</div><div>of catalysts, were selected and studied in more detail for the selected use cases. The relatively fast GFN2-xTB</div><div>method was used to calculate these descriptors and a comparison was done against DFT calculated descriptors.</div><div>ChemSpaX is open-source and aims to bolster the efforts of the scientific community towards data-driven material</div><div>discovery.</div>

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High-throughput immunoassays for SARS-CoV-2, considerable differences in performance when comparing three methods

10.1101/2020.05.22.20106294 ◽

2020 ◽

Cited By ~ 1

Author(s):

Oskar Ekelund ◽

Kim Ekblom ◽

Sofia Somajo ◽

Johanna Pattison-Granberg ◽

Karl Olsson ◽

...

Keyword(s):

High Throughput ◽

Rapid Test ◽

Performance Criteria ◽

Clinical Use ◽

Rt Pcr ◽

Regulatory Authorities ◽

Flow Test ◽

Lateral Flow Test ◽

High Level ◽

Positive Results

Background: The recently launched high-throughput assays for the detection of antibodies against SARS-CoV-2 may change the managing strategies for the COVID-19 pandemic. This study aimed at investigating the performance of three high-throughput assays and one rapid lateral flow test relative to the recommended criteria defined by regulatory authorities. Methods: A total of 133 samples, including 100 pre-pandemic samples, 20 samples from SARS-CoV-2 RT-PCR positive individuals, and 13 potentially cross-reactive samples were analysed with SARS-CoV-2 IgG (Abbott), Elecsys Anti-SARS-CoV-2 (Roche), LIAISON SARS-CoV-2 S1/S2 IgG (DiaSorin) and 2019-nCOV IgG/IgM Rapid Test (Dynamiker Biotechnology Co). Results: All assays performed with a high level of specificity; however, only Abbott reached 100% (95% CI 96.3-100). The pre-pandemic samples analysed with Roche, DiaSorin and Dynamiker Biotechnology resulted in two to three false-positive results per method (specificity 96.9-98.0%). Sensitivity differed more between the assays, Roche exhibiting the highest sensitivity (100%, CI 83.9-100). The corresponding figures for Abbott, DiaSorin and Dynamiker Biotechnology were 85.0%, 77.8% and 75.0%, respectively. Conclusions: The results of the evaluated SARS-CoV-2 assays vary considerably as well as their ability to fulfil the performance criteria proposed by regulatory authorities. Introduction into clinical use in low-prevalent settings, should therefore, be made with caution.

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