Tiled PCR for NGS

PCR Solutions

PCR is an important step in DNA/RNA research. Especially during the pandemic the use of PCR was important.  MBS (molecular Biology Systems) developed the NextGenPCR, a PCR that is faster than the conventional PCR. This is because of the three separate temperature zones of the system, eliminating the ramping time. Complementary PCR kits are developed for COVID and Monkeypox, yet every workflow can be used on the NextGenPCR. 

Variant detection is now very important, so there will not be a new outbreak of a new COVID variant and we likewise there is a wish control Monkeypox. Using Nanopore sequencing technology and the amplicon tiling method, this is possible in a quick and cost efficient manner.

Contact us for questions, or if you want to implement your workflow in this cost and time efficient manner

 

Monkeypox virus (MPXV)

The analysis of Monkeypox starts with a swap of the infected skin. The sample of this swab contains a lot of other DNA particles (impurities) besides Monkeypox. Monkeypox is just 1% of your sample. Therefore it is important to amplify this part of your sample. Using tiled PCR, Monkeypox is amplified and the impurities are now a minor fraction. The NextGenPCR is ideal to perform tiled PCR, due to its 3 separate temperature zones, which can be customised in temperature and heating time. A pre-mixed primer pool and a library prep kit have been developed for Monkeypox, and works ideally on the NextGenPCR.

Go to the Monkeypox library prep kit

Save 94% in costs

By using Tiled PCR before sequencing, cartridges can be efficiently used. With Monkeypox it is possible to read 24 samples on 1 cartridge, instead of 1 sample per cartridge, without using tiled PCR. This way you save 94% in costs with over 98% coverage. This solution can of course also be applicable for other samples, like HLA typing, COVID, and more.

The composition of the oligonucleotide primer panel was developed by Martin Schou Pedersen from the Department of Clinical Microbiology at Rigshospitalet, Copenhagen University Hospital, Denmark and the NextGenPCR® MPXV library preparation protocol was tested on 40 samples in close collaboration with Matthijs Welkers and Marcel Jonges from the Dept. of Medical Microbiology & Infection Prevention at Amsterdam UMC (location AMC), The Netherlands.

 

Corona Virus

As the first waves of SARS-CoV-2 have been passed, it is still important to keep track of the virus. For the analysis of SARS-CoV-2 it is especially important to perform variant detection. Using the NextGenPCR SARS-CoV-2 detection and variant surveillance can be performed using the fluorescence probe based screening method and the variant Nanopore sequencing solution respectively. 

 

Variant detection of SARS-CoV-2

Get your results of 96 samples in just 3.5 hours instead of 7 hours. Increase your daily output from 1 plate to 4 plates per day.

Fluorescence probe screening

In a 27-minute workflow, results of 96 samples are retrieved. The workflow can be performed in such a short time, due to the elimination of the extraction step and the use of a PCR system without ramping times. Two amplicons, one specific for Orf1ab and another for the N-gene are used. Target sequences of the DNA are detected by specific probes, labelled with fluorescence reporter and quencher dyes. The human RNase P probe is labelled with Cy5, and both SARS-CoV-2 probes are labelled on the 5-prime end with FAM.

Go to the SARS-CoV-2 kit

Look also for our other PCR and NGS related solutions. From plastics to instruments and from enzymes and kits to controls for your assays:

Nanopore Technology

Nanopore is a technology that sequences DNA and RNA in real time. On the end of the DNA or RNA strand there is a motor protein and the adaptor sequence. Tethers around the Nanopores, captures the DNA/RNA strand and lead them to the Nanopore. The DNA strand is split and a single strand goes through the Nanopore. The strand provides a disruption in the ionic current in the membrane, by this manner the sequence can be read.

nanopore

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