Making genotyping cheaper and easier

Reference: CTP_FCR_2019_4

This student is to be registered with theUniversity of Nottingham.

Lead academic supervisor: Dr Richard Harrison, NIAB EMR
University supervisor: Dr Matt Loose, University of Nottingham

 Background

The opportunity to capture the full spectrum of genetic variants in any given species is crucial, as this allows accurate classification of individuals and the more accurate linkage of causal variants to phenotypes. There are now a plethora of tools and techniques that allow differential profiling of variant types, from single nucleotide polymorphisms, to DNA base modifications. The challenge is to develop approaches that are easier to execute and analyse.

Objectives

This studentship will aim to develop both laboratory and bioinformatics techniques to capture the full spectrum of genetic variants using a variety of biological models with modifications of agronomic importance that require the development of specific tests to study non-standard genetic modifications.

Approaches

The research work will be divided into upto four workpackages (WPs), each with clear deliverables. These may include:

  1. WP1: SNP panel construction- work to identify a low-cost method for SNP evaluation using single-molecule sequencing
  2. WP2: Epi-allele identification using single molecule sequencing- using Phytophthora fragariae as a model of epiallelic variation
  3. WP3: Structural variant tracking- using Fusarium formae specialis structural rearrangements to identify dynamic genomic rearrangements
  4. WP4: k-mer and signature-based identification- reference free approaches of tracking allelic variation using single molecule sequencing.

Applying for this studentship

The most important eligibility criterion for this funded studentship is residency:

  1. UK students: If you have been ordinarily resident in the UK for three years you will normally be entitled to apply for a full studentship, covering tuition fees and a maintenance stipend.
  2. EU students: If you have been ordinarily resident in another EU country (outside the UK) for three years you will normally be able to apply for a tuition fees-only award (without a maintenance stipend). If you have lived in the UK for three years you may be eligible for a full studentship.

This eligibility is unaffected by Brexit. The UK Government has guaranteed EU eligibility for Research Council funding for PhDs beginning before the end of the 2019-20 academic year.

Anyone interested should contact the FCR-CTP administrator for an application form and return the form to the FCR-CTP administrator before the deadline of 30th April 2019.