BaseClear has received one of the first GridION sequencing systems from Oxford Nanopore Technologies (ONT). With this system, BaseClear can soon offer revolutionary Nanopore sequencing services. BaseClear is the first commercial party in the world to go through the process to be approved as ONT service provider. The expectation is that this will be ready after the summer.
Since BaseClear will soon offer commercial services using Nanopore sequencing technology, a world of new applications will be available. Danny Duijsings, R&D Director at BaseClear, explains:
“The Nanopore technology is based on pulling DNA molecules through very small holes. As the DNA molecule moves through such a hole, you can see what the DNA molecule exactly looks like. Other sequencing technologies use complex biochemical reactions. Another disadvantage of current NGS sequencers is that they can only read relatively small pieces of DNA, and the further you read, the more errors are occurring. Nanopore technology does not have these limitations: actually the length of the piece you can read is only limited by the length of the DNA molecule itself, up to tens of kbp’s. Thanks to this, we can unravel very large and complex genomes, such as the tulip genome. With the Nanopore technology we will also soon be able to read additional information stored in DNA, the so-called epigenetic information. Additionally, new developments will allow us to directly read the mRNA, the less stable copies of the DNA that play an essential role in the cell, without complicated tricks to convert the RNA into cDNA that can introduce bias or errors.”
OVER TWO YEARS OF EXPERIENCE
BaseClear has been working with Nanopore sequencing technology for internal projects for more than two years. Until now, BaseClear has used the little brother of the GridION, the MinION sequencing system, also known as the USB-stick sequencer. Adalberto Costessi, Product Manager NGS at BaseClear, tells more about his experiences with this technology:
“Working with Nanopore sequencing is very exciting, because it combines long read capabilities and a revolutionary real-time analysis. The fact that the read length is only limited by the length of the DNA fragments brings also new challenges compared to short-read sequencing platforms. For Nanopore sequencing, it is crucial that the DNA is as intact as possible and preferably in the tens of kbp’s and longer. And this requirement is literally pushing the physical limits of standard molecular biology techniques, because the simple use of regular lab pipettes and DNA purification columns cause severe fragmentation of the DNA. On the other hand, the real-time analysis can be an extremely useful feature. We don’t need to wait until the end of a sequencing run lasting one or several days before we can analyse the data. On the Nanopore platforms every single DNA read becomes available as soon as it is sequenced, so we can perform real-time downstream analysis, like fast detection and identification of pathogens in a pure or even a mixed sample. We see a lot of interest in this application and we think it has the potential to become a new standard with a true added value.”
Collaboration FG Technologies
The GridION will also be used by Future Genomics Technologies (FG Technologies), the collaboration between BaseClear and Leiden University. FG Technologies will use the GridION to see if new ideas from scientific research can actually work in a practical application. BaseClear focuses primarily on performing routine analyses, such as the genome analysis of bacteria and fungi or for analysing complex microbiological compositions.