Whole human DNA sequencing at VIB on the PromethION from Oxford Nanopore Technologies

14 February 2018
VIB is proud to be the first to report a sequencing output of 63 GB on a single PromethION flow cell in 64 h with a human DNA sample. This is a major leap forward for Oxford Nanopore Technologies (ONT), since this opens the door to use the PromethION, which is still in early access, for full-length human genome sequencing. These results are also a step towards the sub-$1,000 genome, announced by Clive Brown, CTO of ONT, in his webcast last week. The long-read lengths, low sequencing cost, sequencing speed and the high sequencing output that VIB achieved makes ONT a competitor in the current sequencing market.

The generation of the 63 GB sequencing output was a joint effort between the VIB-UAntwerp Center for Molecular Neurology and the VIB Technology Innovation Lab. For many research projects, the long read lengths obtained with ONT are crucial, confirmed Dr. Mojca Strazisar, Expert Scientist in the VIB - UAntwerp Center for Molecular Neurology.  She comments that ‘the long read lengths obtained on the ONT devices provide a unique opportunity to include a comprehensive sequence analysis of structural variants for example duplications or translocations, which were difficult to detect with the current sequencing technologies. Structural variants and the subsequent correlation of variant size and sequence composition with disease onset age, disease progression and other clinic-pathological parameters opens up doors to study fatal neurodegenerative diseases at scaled levels’.

The collaboration between VIB and ONT, started in the beginning of 2014, when the group of Prof. Dr. Christine Van Broeckhoven (VIB-UAntwerp) was granted access to the MinION early-access program, funded through the VIB Tech Watch initiative. Dr. Halina Novak, Technology & Innovation Manager, noted that ‘the promising results with the MinION program and the possibility to scale up to 2400 GBs in one single PromethION run using 48 flow cells in parallel, resulted in a joint-investment by three VIB Centres and VIB Tech Watch in one GridION and two PromethION systems. The result obtained last week proved that it was worth waiting and there is still potential for further scale-up!’ Dr. Wai Long Tam, who is part of the team evaluating the PromethION within VIB is highly enthusiastic about this project since ‘the ONT platforms are developing at a rapid pace and it is truly exciting to be at the forefront of this research. At VIB, we are exploring the technology in depth since obtaining long reads is highly advantageous across the different fields in life sciences. VIB applications range from sequencing plants, frogs, tumors of varying cancer types, neurological clinical sample to microbiome. At the same time, we are also exploring direct RNA sequencing and even targeted sequencing approaches.’

Very exciting times are coming up for the company as well as the ONT community users, since a plethora of new ONT applications will soon be released, ranging from epitranscriptome and epigenome analysis and single cell sequencing methods. A whole new field of applications using ONT technology might be opened, since Clive Brown referred to DNA synthesis in his webcast last week. He also gave some hints  on some new platforms including Zumbador and Voltrax V2, but we will have to wait until the London Calling meeting in May to discover all the details.

The first full-length human genome sequencing results using the ONT MinION platform were published by Nick Loman and Matthew Loose in Nature Biotech two weeks ago, and required 39 MinION flow cells to reach ~ 30 X coverage. Based on our output, 40 X coverage can be obtained using two PromethION flow cells. In addition, as higher sequencing outputs were already obtained in-house by ONT and with the newer versions of the flow cells being developed, it is expected that the output will continue to increase.

ONT technology evaluated by Tech Watch initiative
Early-access to the PromethION and GridION platforms at VIB were granted by the VIB Tech Watch initiative, and both instruments are now installed for evaluation by the ‘Technology Innovation Lab’ in the VIB centers. In this set-up, the ‘Technology Innovation Lab’, together with the groups and core facilities, boost the uptake of new technologies within VIB. Next to this, the Innovation Lab also optimizes experimental set-up and troubleshoots with the VIB groups where needed, to rapidly boost technology uptake across the institute.

ONT technology evaluated by VIB-UAntwerp Center for Molecular Neurology
VIB’s Center for Molecular Neurology aims to increase our understanding in neurological disease processes. The embedded Neurodegenerative Brain Disease (NBD) group and Neuromics Support facility used their state of art expertise in genomics to optimize the use of the ONT platforms. This technology is particularly important for the research in neurodegenerative diseases such as Alzheimer’s and could potentially lead to development new medications and treatments.