High quality long read sequencing from low input DNA

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

Genomics is a fast-moving field that is constantly been driven forward by developments in sequencing technology. To stay at the leading edge of this field it is important that we invest periodically in the latest equipment. In this application the Centre for Genomic Research (CGR) at the University of Liverpool proposes to purchase a Pacific Biosciences Sequel II and a FemtoPulse system to extend its current sequencing provision. These instruments will provide new, unique capability-- generation of long-read DNA sequence data from limited amounts of DNA, enabling new applications in de novo genome assembly, microbiome analysis, AMR and gene regulation. The CGR has a long-track record of successfully running PacBio long-read sequencing platforms and of supporting the research community by providing access to genomic technologies. The Sequel II will be placed in an established laboratory, with 20 staff and ~£5m of equipment. Our experience with PacBio platforms specifically means that the Sequel II can be deployed immediately on arrival, replacing our Sequel I platform, which will soon be uneconomical, unable to meet researchers' expectations, and hence functionally becoming obsolete.

Technical Summary

The Centre for Genomic Research (CGR) at the University of Liverpool has provided DNA sequencing and analysis services to the UK research community for over 10 years. The CGR is one of the largest facilities of its type in the UK, with a core staff of 20 people. As a facility, the CGR handles over 300 projects per year, ranging from small pump-priming / R&D projects to large scale projects. The current sequencing infrastructure within the CGR comprises Illumina (Novaseq 6000 and MiSeq), Oxford Nanopore and PacBio sequel. As such, the CGR offers access to high-throughput sequencing technologies and applications thereof to a large number of projects that are aligned with the major strategic priorities of the BBSRC (e.g. pest control, crop and livestock genomics/transcriptomics, metagenetics/metagenomics).
This proposal seeks to refresh our long-read sequencing platforms with the purchase of a PacBio sequel II. The last two years have seen real improvements to the technology and a re-assessment of the strengths of the platform providing high quality and high throughput sequencing. The current Sequel is therefore set to become obsolete as it is superseded by the increased throughput, increased accuracy and reduced cost of the Sequel II. These enhanced features also enable new biological questions to be addressed for the first time by the Sequel II.
We therefore believe that the time is opportune for the CGR to apply the technology to projects within the BBSRC's remit. To achieve this, we have brought together a group of Investigators from Liverpool with a strong track-record of BBSRC funding. In addition, and in order to demonstrate the breadth of science and critical mass of users, we have received 30% support from the University of Liverpool for the purchase of a PacBio Sequel II system and auxiliary equipment (Agilent FemtoPulse). We will also promote uptake by academic and industrial partners though marketing and training/workshop activities.

Planned Impact

We propose explicit outreach and training activities to bring information on the capabilities and capacity available through the Centre for Genomic Research to potential users and other stakeholders. The Investigators' key strengths are in genome sequencing, genomic technology and bioinformatics and we aim to make an impact from our research through:
1. Assisting collaborators in pump-priming work, in designing experiments, in applying for funding and in publishing their results, depositing data in public repositories, and exploiting commercial potential of findings. Researchers working with the CGR benefit from having trained staff handle their project and having access to cutting edge equipment. We will therefore have an impact on many different disciplines in basic and applied sciences and on the research councils and charities that fund them.
2. Working with The University of Liverpool's Business Gateway to identify potential areas for commercial exploitation of the work handled though the CGR. We have also embedded a project/business manager within the CGR to drive this area forward. 2. Reaching out to the research community and the general public through formal and informal presentations, marketing material and social media. In this, we will utilise the effective press communications systems within the University of Liverpool to communicate our work to wider audiences, and use public forums such as open days, social media and our website to further publicise our work. The CGR is also part of a wider UK community of academic service laboratories with whom we co-organise the annual UK Genome Science Meeting, to ensure the relevance and reach of what the CGR offers as a facility.
3. Training of researchers in the applications of next generation sequencing through targeted training events in collaboration with our partners in the N8 and other universities. There is a recognized skills gap in next generation sequencing training provision. The CGR is committed to running at least three annual training courses per year coordinated and delivered by a dedicated training bioinformatician: (1) Master classes, aimed at researchers of all seniorities and delivering an overview of the technologies, their applications, the core algorithmic underpinnings of next-generation genomics analysis, as well as hands-on experience in using some of the analytical tools. (2) Bespoke training focused on reaching the coming generation of researchers: PhD students, postdoctoral researchers and early career fellows and lecturers. This will include hands on experience of next generation sequencing, in depth training in the key analytical technologies, and a programme of lectures on applications from guest lecturers and specialists.
4. Encouraging all CGR staff and staff associated with research grants led by the Investigators to be actively involved in these activities. In addition, the CGR is active in training PhD students and postdocs. There are ~20 PhD students working within the CGR and we run numerous courses and give presentations on our science internally and externally.
5. Working closely with the technology platform providers to drive innovation and test new methodologies and applications. The CGR has a close working relationship with Illumina and PacBio, acting as a reference site and certified service provider for applications. We will also continue to host manufacturer-led seminars as events aimed at providing networking opportunities between academics and commercial partners.
6. Benefiting industry by providing a complete service for contract sequencing and bioinformatics. This raises the competitiveness of UK companies and therefore helps employment within the UK. As demonstrated with our Unilever partnership (see supporting letter)

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