A multi-channel liquid handler for the Bristol Genomics facility

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences

Abstract

Genomics technologies, specifically sequencing and genotyping, continue to witness exciting developments in both increased scale and reduced costs.

The Bristol Genomics Facility collaborates closely with a number of groups at Bristol including the Cereals Functional Genomics group , who remain at the cutting edge of technology development; via collaborations with Affymetrix and LGC a number of commercially successful products have been developed and utilised such as the Axiom 820K wheat high density array and the Axiom 35K wheat breeders array. These developments have resulted in Bristol becoming a centre of high throughput genotyping for multiple commercially important species following the installation of a 384-well Axiom GeneTitan high throughput genotyping platform in 2014 (ALERT 13). In 2015 the University provided funds for the facility to purchase both an Illumina MiSeq and NextSeq500 next generation sequencer. These various developments have resulted in the Facility processing over 120,000 DNA samples over the past four years. To continue to be at the forefront of technology development and application the Facility must maintain and improve its post-PCR sampling handling provision and procedures so that it is able to cope with the ever increasing demand for its services. Provision of a high throughput liquid handling instrument would enable to Bristol Genomics Facility to both develop new strategies (such as targeted genotyping by sequencing) and expand the number of applications that it can offer its internal and external users.

Technical Summary

Funds are requested to purchase a post-PCR multi-channel liquid handler together with a 3-year warranty.

The application to purchase the liquid handler has been instigated by Professor Keith Edwards, the academic director of the Bristol Genomics Facility, following discussions with several researchers and industrial partners both at Bristol and beyond. Researchers who would directly benefit from replacing and upgrading the existing facilities at Bristol include Dr Greg Jones' into food safety, Dr Kevin Kemp's research into the ageing brain, Dr Alison Bentley's research into food security at NIAB and Dr Chris Burt's wheat breeding at RAGT to address issues associated with food security.

All of these cases are in addition to Professor Keith Edwards' own extensive research into wheat breeding and its relationship to food security and Dr Gary Barker's research in metagenomics

The scientific cases for support all require high throughput sequencing and genotyping; the high throughput sample handling suite enables this on a scale required for genome wide applications such as genotyping by sequencing and genome scanning.

The Biomek i7 Multichannel Workstation is the most powerful and comprehensive Biomek available and it is the only high throughput liquid handling platform validated and approved by Thermofisher for the automated processing of Axiom High Throughput 96 & 384 format genotyping arrays (see email from Thermofisher). In addition, the Biomek i7 supports and complements a variety of other genomic applications run by the genomics facility including high throughput expression arrays and the support of automated next generation sequencing library construction methods. This is in addition to general post-PCR processing steps including nucleic acid quality control and quantitation, nucleic acid purification and size selection for example.

Planned Impact

The purchase of the post-PCR high throughput sample handling robot will have a significant impact on many of the users of the Bristol Genomics Facility, specifically on their ability to carry out cost effective high throughput sequencing and genotyping. As the Facility is open to all users both within and beyond the University (non-Bristol users have included the John Innes Centre, Rothamsted Research, Nottingham University and Aberystwyth University), installation of the suite will impact on the maximum number of researchers possible and enable research across a wide area of the scientific portfolio of the BBSRC, including wheat, humans and a range of other species of relevance to the BBSRC.

As the wheat breeding company RAGT has indicated that they will make use of the suite if it is installed at Bristol, the impact of the purchase will extend beyond the academic environment and hence could have a significant on the ability of UK wheat breeders to develop the next generation of elite wheat varieties having improved agronomic traits such as enhanced disease resistance and/or increased yield.

The Edwards group has an excellent track record of generating science with impact, for instance, it has recently delivered to the wheat breeders a large amount of genomic sequence, and a large number of SNP markers (>820,000 to date), all in a usable form and without any associated IP (via the public database held at CerealsDB). In addition, it has, and continues, to work with the genotyping company's Affymetrix and LGC to develop further molecular markers, which are being used by both companies to provide commercially successful services to wheat breeders and academics alike (see the web site of both companies for further details). The current BBSRC funded WISP has continued to develop further SNP resources further and has on its steering committee, all the major wheat breeding companies. In recognition of Prof. Edwards' contribution to UK agriculture the Royal Agricultural Society of England awarded him their 2011 Research Medal, a Medal which acknowledges "research work of outstanding merit, carried out in the United Kingdom, which has proved or is likely to be, of benefit to agriculture". In addition, in 2018 Prof. Edwards was jointly awarded (with Prof. Graham Moore, JIC) the Rank prise for nutrition, for his contribution to global wheat breeding via the provision of a wide range of SNP-markers and genotyping platforms.

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