NovaSeqX Plus: short-read sequencing at the Centre for Genomic Research
Lead Research Organisation:
University of Liverpool
Department Name: Faculty of Health and Life Sciences
Abstract
Successive advances in DNA sequencing technology have driven an explosion in genomics research over the last decade or more and has become an essential tool to answer questions in bioscience more generally. UK science has an enviable place at the forefront of genomics but to maintain this position it is essential that it invests in new DNA sequencing technology as it emerges.
The proposal here is to purchase an Illumina NovaSeqX Plus sequencing platform, which is a new machine from the market leader in DNA sequencing and which makes its previous machine obsolete. It can produce 16Tbp (16,000 trillion letters of genetic code) in the space of 48 hours and for around one third of the cost from the previous machine. This allows us to do more and better science. Genomics experiments are now cheaper, which allows more researchers to use the technology within their research budget. It allows researchers to perform bigger experiments that have more samples to give more rigorous results. Finally, it allows new experiments to be performed that would otherwise be out of reach due to cost, these include looking at the way thousands of genes are switched on and off across thousands of individual cells or to deep sequence DNA from complex communities of bacteria or viruses.
The equipment will be placed in the Centre for Genomic Research at the University of Liverpool, which has a well-established track record in offering genomics expertise and DNA sequencing to the UK community. It is the largest sequencing facility within a UK university and, unlike many facilities, supports a lot of non-medical work, making it particularly well-suited to supporting research in the BBSRC remit. It will be used for a range of applications, including crop improvement, controlling animal disease, understanding fundamental biology and developing new methods or technologies. It will also act as infrastructure to support UK industry and to maintain pandemic preparedness.
We will help users access the technology by providing advice on experimental design, support with data analysis and training workshops on genomics. The DNA sequence data produced be made available to researchers worldwide using publicly available repositories. The careers of our staff will be supported by increased job security and skill development, and this lets us retain their important technical expertise. The equipment will allow us to reduce our environmental impact because it uses less plastic waste and lower transport costs from reagents that now no longer have to be shipped on dry ice.
The proposal is good value for money because (i) the DNA sequencing is much cheaper than previously, (ii) we able to offer the service widely, so making good use of the machine capacity, and (iii) we are able to provide other expensive equipment in our laboratory required to run the equipment effectively in preparing samples and processing data.
The proposal here is to purchase an Illumina NovaSeqX Plus sequencing platform, which is a new machine from the market leader in DNA sequencing and which makes its previous machine obsolete. It can produce 16Tbp (16,000 trillion letters of genetic code) in the space of 48 hours and for around one third of the cost from the previous machine. This allows us to do more and better science. Genomics experiments are now cheaper, which allows more researchers to use the technology within their research budget. It allows researchers to perform bigger experiments that have more samples to give more rigorous results. Finally, it allows new experiments to be performed that would otherwise be out of reach due to cost, these include looking at the way thousands of genes are switched on and off across thousands of individual cells or to deep sequence DNA from complex communities of bacteria or viruses.
The equipment will be placed in the Centre for Genomic Research at the University of Liverpool, which has a well-established track record in offering genomics expertise and DNA sequencing to the UK community. It is the largest sequencing facility within a UK university and, unlike many facilities, supports a lot of non-medical work, making it particularly well-suited to supporting research in the BBSRC remit. It will be used for a range of applications, including crop improvement, controlling animal disease, understanding fundamental biology and developing new methods or technologies. It will also act as infrastructure to support UK industry and to maintain pandemic preparedness.
We will help users access the technology by providing advice on experimental design, support with data analysis and training workshops on genomics. The DNA sequence data produced be made available to researchers worldwide using publicly available repositories. The careers of our staff will be supported by increased job security and skill development, and this lets us retain their important technical expertise. The equipment will allow us to reduce our environmental impact because it uses less plastic waste and lower transport costs from reagents that now no longer have to be shipped on dry ice.
The proposal is good value for money because (i) the DNA sequencing is much cheaper than previously, (ii) we able to offer the service widely, so making good use of the machine capacity, and (iii) we are able to provide other expensive equipment in our laboratory required to run the equipment effectively in preparing samples and processing data.
Technical Summary
We will purchase and install an Illumina NovaSeqX Plus DNA sequencing platform. Its key advantage is to produce 3x the data for the same price as the previous technology. More researchers will therefore be able to afford to use genomics in their studies, thereby broadening the reach of genomics. It also enables researchers to perform previously inaccessible methods that require either increased numbers of samples (GWAS and population scale sequencing) or increased depth of sequencing (metagenomics and single-cell genomics).
The equipment will be embedded within the Centre for Genomic Research (CGR), University of Liverpool, which is a well-established centre offering the latest genomics technology and advice to researchers across the UK. Unlike other sequencing facilities, the CGR is not highly medically focussed, which makes it well-suited to supporting a large body of bioscience research within the BBSRC remit on crops, non-model species and pathogens. It has expertise in a wide range of genomics methods, including whole genome sequencing, RNAseq, epigenetics and single-cell genomics. The equipment will replace a now obsolete previous model and allow us to continue to offer the latest genomics technology to UK researchers. It will be able to rapidly support researchers since it can slot immediately into a range of existing workflows used in the CGR, which are implemented on automated pipetting platforms under clear SOPs.
We have a clear, end-to-end plan to support users in accessing the technology, beginning with a dedicated enquiry team able to offer advice on study design, to experienced laboratory staff able to process challenging samples across a range of application, to a bioinformatics team able to provide help with data analysis.
The equipment will reduce environmental costs of packaging and transport because reagents can now be shipped at ambient temperature rather than on dry ice. Plastic waste is also reduced through recyclable cartridges.
The equipment will be embedded within the Centre for Genomic Research (CGR), University of Liverpool, which is a well-established centre offering the latest genomics technology and advice to researchers across the UK. Unlike other sequencing facilities, the CGR is not highly medically focussed, which makes it well-suited to supporting a large body of bioscience research within the BBSRC remit on crops, non-model species and pathogens. It has expertise in a wide range of genomics methods, including whole genome sequencing, RNAseq, epigenetics and single-cell genomics. The equipment will replace a now obsolete previous model and allow us to continue to offer the latest genomics technology to UK researchers. It will be able to rapidly support researchers since it can slot immediately into a range of existing workflows used in the CGR, which are implemented on automated pipetting platforms under clear SOPs.
We have a clear, end-to-end plan to support users in accessing the technology, beginning with a dedicated enquiry team able to offer advice on study design, to experienced laboratory staff able to process challenging samples across a range of application, to a bioinformatics team able to provide help with data analysis.
The equipment will reduce environmental costs of packaging and transport because reagents can now be shipped at ambient temperature rather than on dry ice. Plastic waste is also reduced through recyclable cartridges.
Organisations
| Description | A new DNA sequencing machine -- an Illumina NovaSeqX Plus -- was installed and made operational at the Centre for Genomic Research, University of Liverpool in November 2023. It has been applied to a number of systems within the BBSRC remit of food security of basic bioscience, including soli microbiomes, corn and livestock parasites. It has also been used in projects involving mosquitos (as vectors of disease) and of wildlife populations threatened by climate change. It supports the NERC Environmental Omics Facility, which has recently been renewed for a further 7 years. It is available to industry; we already work closely with Unilever and we are working with innovation consultants (LYVA labs) to increase visibility of the resource within the NW region. The advantage for collaborators and UKRI is that it reduces the costs of sequencing. This allows projects to either be delivered more cheaply or to increase the scope of experiments. In particular, it enables new discoveries through population-level sequencing. |
| Exploitation Route | The equipment is broadly applicable across the biological remit. We expect it to enhance basic research in animal health, agriculture, microbiome science and biodiversity research and to support academic researchers in those fields accordingly. We also expect it support industry, particularly within the Life Sciences in NW England. Finally, it also provides infrastructure that is useful for disease surveillance and support to UK government and international agencies in public health. |
| Sectors | Agriculture Food and Drink Environment Healthcare |