The Oxford Genomics Centre is a genomics service facility based at the Wellcome Trust Centre for Human Genetics (WTCHG), a research institute of the Nuffield Department of Medicine at the University of Oxford.

Genomics technologies, in particular high-throughput sequencing and micro-array-based applications, have revolutionised modern genetics. Sustaining capability and expertise in these technologies is a strategic priority for the WTCHG, and underpins the objectives of the Oxford Genomics Centre in providing expert advice and high-quality services to scientists within the Centre, at the University and further afield. We have a particular remit to support excellent research within WTCHG and certain collaborating institutes: please contact us for more information.

Our comprehensive offering of genomics applications in sequencing, arrays and single-cell isolation and analysis is sustained by many of the latest commercial technology platforms, including Illumina and Oxford Nanopore sequencing, Illumina and Affymetrix arrays, Fluidigm and Sony cell isolation, Labcyte and Beckman automation platforms and the 10X Genomics Chromium platform.

We operate on a cost-recovery basis for academic projects, and we offer competitive rates for commercial organisations. Please contact our Project Management team for more information about the services available to different sectors of the research community.

Who are we?

 


 

Process Improvement

The Oxford Genomics Centre supports the scientific efforts of our users and external customers by always working to improve the efficiency and reliability of our processes, by adopting new platforms and techniques, and by working with other groups to develop optimised methods.

Particular areas of effort and achievement include the automation and miniaturisation of library prep methods for sequencing; the adoption of high levels of automation for array processing; the introduction of new platforms and highly automated, miniaturised methods for single-cell analysis; and the development of automated processing and analysis pipelines for sequencing data.

 

In recent years we have witnessed an exciting explosion of technologies and applications that has attracted more researchers to utilise genomics platforms. The Oxford Genomics Centre has established a process improvement initiative so that we can continue to provide and support cutting-edge technology. The goal is twofold:

  • to identify methodologies or technologies that can expand our portfolio of supported applications; and
  • to improve the current performance of the group by being faster, cheaper and delivering better quality data.

The challenge of increased data output per sequencing lane has led to the development of multiplexing (up to 96 samples in one lane), which in turn has increased the number of genomic libraries processed. We have evaluated and modified each step of the workflow to reduce library preparation costs and maximise the number of samples produced from every kit. Our target is to reduce costs even further, and new strategies are under investigation and evaluation.

Read more about our current sequencing platforms.

To increase throughput a key aspect of our workflow has been the use of Beckman liquid handlers, of which the group has four. A significant effort has been put into implementing automation for different workflows.

  • Library preparation was custom automated for: gDNA, ChIP and mRNA which represent the majority of library types for sequencing (~85%).
  • Further automation was developed for QC and quantification steps which has reliably increased accuracy and reduced hands-on time.

As part of a continuous drive to improve upon turnaround times, we have been working to implement the use of robotics to set up the PCR reactions which are the most time-consuming part of the operation.

We are constantly evaluating ways to automate the calculation of summary statistics used in the reports.

We have improved the content of the reports provided to customers on completion of a project, allowing the user to assess the success of a project ‘at a glance’, and have added more details on the way in which the data is assessed, edited and interpreted. The statistics generated for the reports help us carefully track the performance of the processing, and identify any technical errors should they occur.

Read more about our current Array platforms.

The analysis of high-throughput genomics data presents many challenges for data analysis. While for many tasks there are high quality tools available, in other areas we have developed tools to increase the accuracy of analysis or to provide a wider range of analysis options.

Methods developed by members of the BSG team have been widely used in other centres and in international projects, including the 1000 Genomes Project.