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Developing Next-Generation Sequencing multiplexes for Birds of Prey: A pilot study for non-human forensics and conservation biology

(This project has been filled - no further applications will be accepted)

Project Supervisor: Dr Celia May

Co-supervisor: Prof Mark Jobling & Dr Jon Wetton

Non-academic partner: Nicola Oldroyd, Illumina

PhD project title: Developing Next-Generation Sequencing multiplexes for Birds of Prey: A pilot study for non-human forensics and conservation biology

Project outline:

The analysis of DNA variation in biological samples is a cornerstone of forensic science and was founded at Leicester with the discovery of individual-specific DNA fingerprints in 1984. While most forensic activity focuses on human DNA, analysis of animal and plant DNA also contributes by linking locations, or providing species- or individual-level identification, for example in the context of wildlife- and eco-crime.

Since the 1990s, individual-level analyses have been based on length differences at short tandem repeat (STR) loci as ascertained by capillary electrophoresis, whilst traditional Sanger sequencing of mitochondrial DNA (mtDNA) has determined ancestry and species-level identification. However over the last decade, next-generation sequencing (NGS) has revolutionised biology allowing cost-effective characterisation of whole genomes; this holds great promise as the next innovation in forensic analysis too. Illumina has developed a human forensic NGS kit that allows simultaneous testing of multiple autosomal and Y-specific STRs, mtDNA and single nucleotide polymorphisms (SNPs). This multi-target approach conserves biological material whilst maximizing discrimination and efficiency. This same approach could be applied to animal and plant forensic evidence allowing both human and non-human tests to be performed using a common platform, bioinformatics pipeline, and ultimately reporting procedure.

This iCASE studentship will explore the approach as applied to birds of prey. Theft from the wild for resale to the falconry trade is a lucrative business and DNA testing via classical approaches has already led to many court cases in the UK. However, nowadays, forensic service providers cannot support such specialised tests. We have already identified candidate STRs that could be incorporated into an NGS-based multiplex. These will be supplemented using the recently published whole genomes of the peregrine, saker and bald eagle along with emerging genomes from the 10K Genomes Project. MtDNA targets for species identification will also be included. The project will involve mutation rate analysis to establish exclusion probabilities, creation of population reference databases, and multiplex design, validation and implementation on the Illumina MiSeq FGx Forensic Genomics System. Since birds of prey are indicator species of the environment, the developed multiplexes may also be a useful tool for molecular ecologists and conservation biologists.

The industrial partner Illumina is a global leader in genomics, developing and manufacturing platforms and associated consumables as well as providing bioinformatics solutions for modern day analyses of genetic variation. Illumina is world renowned for it NGS technology that has revolutionised the study of not only whole genomes, but also exomes, transcriptomes and methylomes. The successful applicant will undertake a placement within Illumina’s UK specialist forensic genomics division.

To reflect industry practice, a performance-dependent annual supplement to the student stipend may be negotiated with Illumina after the first year. Travel and subsistence costs for attendance at and support of Illumina sales and marketing events will also be met.

Techniques that will be undertaken during the project:

  • bioinformatics; screening publically available resources to identify suitable targets, developing appropriate pipelines for the NGS interpretation, specifically in the context of forensic analysis and case reporting
  • DNA extraction: from variety of substrates (blood, feathers, egg-shells, etc.)
  • multiplex PCR; design and validation of novel plexes
  • sequencing; traditional Sanger and Illumina MiSeq NGS approaches
  • STR profiling; capillary electrophoresis using fluorescently-tagged primers

Interview date: TBA