Bioscience for sustainable agriculture and food

Category: Industry Co-funded Studentships

Forensic field sensing of nucleic acids using nanopore sequencing

Project No. 2271

Primary Supervisor

Dr Franklin Nobrega – University of Southampton

Co-Supervisor(s)

Dr Erik Garrison – University of Tennessee Health Science Center, Memphis, USA

Industry Partner

Dr David Mittleman CEO Othram Labs (USA),

Summary

Rapid in-field sequencing of DNA samples is useful for forensic science, such as in the identification of familial relations of unidentified individuals.

In-field sequencing can also provide information critical to other aspects of forensic investigation, such as information about bacterial community and environmental disturbance or state. A method that integrated a sequencing system into a compact, user-friendly suitcase-based lab would be of great utility in forensics.

In this project, the student will develop a nanopore sequencing-based technique for the sequencing of low DNA amounts with the purpose of direct analysis of forensic samples (e.g. blood, semen, buccal swabs), mitochondrial DNA analysis, SNP and STR analysis, familial identification, and microbial identification for bioterrorism and geolocation. The establishment of the technique will further involve the optimisation of library preparation methodologies and the development of novel data analysis pipelines. The technology developed will have an impact in forensic investigation, and will additionally have critical value to agricultural work.

The project offers the student an opportunity to learn both dry-lab and wet-lab skills, highly relevant to a career in academic or industry. The student will work with a number of groups at the universities of Southampton and Tennessee Health Science Center, offering expertise in different areas and enabling world-class doctoral training. The student will receive training in microbiology, genomics, and bioinformatics. Relevant wet-lab techniques include short- and long-read sequencing, in situ sequencing, extraction of low amounts of DNA from variable samples, library preparation, and basic molecular biology techniques. Dry-lab techniques include scalable computational systems to infer genomes from DNA and sequencing data, metagenome analysis, detection of genotype genomic variants, pangenome mapping and genotyping, and graphical modelling of pangenomes. The student will additionally have the opportunity to apply the system developed to engage in field tests in forensics-related and simulated agricultural applications. The majority of these skills will be learned via osmosis from other team members and the supervisory team, but the student will be encouraged to attend external courses and workshops.