Adapting Existing Technologies to Develop Custom Applications and Solutions at a Core Genomics Facility

A snapshot of the video from Labcyte Genomics Symposium 2016

Wellcome Trust Centre for Human Genetics Wellcome Trust Centre for Human Genetics is a research institute of the Nuffield Department of Medicine at the University of Oxford, funded by the University, the Wellcome Trust and numerous other sponsors.  

Dr. Paolo Piazza, section leader for Library Prep and Process Improvement at the Wellcome Trust Centre for Human Genetics, at the Oxford Genomics Centre, spoke at the Labcyte Genomics Symposium about automated solutions for sequencing facilities.

The Wellcome Trust Centre for Human Genetics is a core facility that provides a high-throughput genomics and bioinformatics service. The Oxford Genomics Centre provides access to research and development capabilities with expertise in three main areas: arrays (genotyping and expression analysis), single cell genomics and Illumina sequencing; it is in this last area of application that Dr. Piazza’s section develops custom workflows and solutions.

In this video presentation, Dr. Piazza presents a selection of the technologies and workflows adapted for various sequencing library applications, with examples of challenges and improvements.

The group undertakes a wide range of low throughput, custom projects for customers and specializes in adapting existing technologies to find solutions, mainly using Illumina sequencing. Dr. Piazza illustrates the diversity of his section’s work with a number of different applications they have worked on involving pathogen resequencing, such as adapting a protocol to detect and sequence full viral genomes. More recently, an additional module to capture pathogen reads has enriched the sequencing data, reducing the number of reads required, minimizing costs whilst providing an alternative to accurately determining viral loads in clinical samples.

A further example is described, showing how the team quickly implements new and promising technologies. In this case, developing a process to detect and evaluate C. difficile on a clinical ward that can deliver data within 1 week rather than several months.

Using newer sequencing technologies

Dr. Piazza also provides an overview of newer sequencing technologies he has been using, such as Oxford Nanopore sequencing, “an exciting technology which allows you to do long reads comparable to Pacific Bio, but instead of large platform, it is smaller and more portable”. Dr. Piazza has been using this technology to support methods for rapid detection of antibiotic resistant pathogens. (Bradley et al., Nature communications 2015). Standardization of workflows in the Library Prep and Process Improvement group is also described, with summaries of the common points and processes for sample QC and library preparation.

Finally, Dr. Piazza reveals how automated liquid handling using the Labcyte Echo 525, has been successfully integrated into these standard workflows. Dr. Piazza is now looking at streamlining library preparation methods to reduce the number of offline steps, initially focusing on the final clean-up step before PCR amplification. PCR amplification here is typically required for pathogen detection applications, which require lengthy culturing steps to generate enough DNA for preparation. Removing the clean-up step would speed up the workflow and also prevent any loss of DNA. Progress has been made to replace final clean-up with a heat inactivation step whilst maintaining the number and quality of sequencing reads possible from libraries. Efforts have also been made to replace DNA fragmentation using an offline sonication with enzyme fragmentation. Data from both of these approaches are presented and the merits of various library kits are discussed, with regard to their ability to produce workflow improvements.

Watch the full presentation or learn more about the Echo^® 555 Liquid Handler
 

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