Protecting the Food Chain by Rapid On-Site Nanopore DNA Sequencing

Adulteration of the food chain with products derived from undeclared species greatly affects consumer confidence, can pose health risks and may involve the illegal exploitation of protected species. High-profile cases such as the 2013 horsemeat scandal increased pressure to improve the reliability and speed of species identification. Unfortunately, current methods for checking the species of origin of raw meats require out-sourced laboratory testing using expensive equipment, which can take up to a week. Similar delays occur when testing for pathogenic microbes, by which time food from potentially contaminated production lines may have already reached retailers and consumers. Species identification is also key in combatting the multi-billion dollar illegal wildlife trade which often involves substitution of species on a massive scale, particularly in commercial fisheries worldwide, and the sale of bushmeat - wild animals caught in developing countries that are butchered and sold in markets.

We seek a highly-motivated student with an interest in genetics, genomics or forensic genetics, whose research project will develop rapid, on-site DNA analysis methods using the Oxford Nanopore Technologies (ONT) MinION portable third-generation sequencing device. The focus will be on mitochondrial barcode genes that show characteristic sequence differences between species; a similar approach can identify bacteria from their 16S rRNA sequences. ONT sample and sequencing preparation devices currently in development, including the VolTRAX microfluidics platform and hand-held disposable DNA library preparation systems will be trialled for utility upon release.
The student will gain an appreciation of the technology needed to ensure food-chain integrity and will be trained in existing approaches to species identification. During the course of the project the student will spend three months working with our industrial partner Cranswick plc exploring how such tests can be integrated into the commercial environment.

Supervision, training and academic environment

You will be part of the Midlands Integrative Biosciences Training Partnership (MIBTP), a BBSRC-funded Doctoral Training Partnership between the Universities of Warwick, Birmingham and Leicester. As an iCASE student, you must fulfil the MIBTP entry requirements and will join the MIBTP cohort for the taught modules and masterclasses during the first term. You can then start your PhD project in Jan 2019 but must complete a 3-month mini-project (at Warwick or Birmingham) before the end of the first year. You will remain as an integral part of the MIBTP cohort and take part in the core networking activities and transferable skills training.

You will be supervised by an experienced team and form part of a dynamic and productive research group studying human and animal genetic diversity, with projects in population genetics, forensics, recombination and mutation biology, and human disease genetics.