The University of Newcastle, Australia

Epigenomics in Multiple Sclerosis

Closing Date: 01 May 2019


PhD Scholarship

This project will involve analysis of MS EWAS data sets currently being generated using the Illumina Epic Arrays. Given the large amount of data involved and the complex computational and statistical models to be applied, this project will be heavily focused on data analysis.

Multiple sclerosis

MS is a common autoimmune disorder that can lead to severe neurological symptoms like such as reduced cognitive function, psychiatric problems and physical disabilities. The disease is complex, arising from the complex interplay of genetic factors and environmental exposures. A major goal in MS research is to understand these gene-environment interactions and to use this information to personalise treatments to improve patient outcomes. Epigenetics is the study of DNA-based factors that can influence gene expression independently of underlying DNA sequence and can be modified by environmental exposures (eg, medicines). As such, epigenetics provides a natural interface for the environment to interact with the genome to influence disease onset, severity and progression. DNA methylation is an one epigenetic mechanism that can now be measured on a genome-wide scale (ie. epigenomics) and has given rise to the epigenome-wide association study (EWAS) design. The MS group at the Hunter Medical Research Institute have been performing MS EWASs for a number of years and have identified a number of exciting findings. Thanks to some newly awarded funding we are now continuing this line of investigation in an effort to identify epigenetic factors that influence MS onset, severity and progression This project will involve analysis of MS EWAS data sets currently being generated using the Illumina Epic Arrays. Given the large amount of data involved and the complex computational and statistical models to be applied, this project will be heavily focused on data analysis. Specifically, the project will involve using a number of different bioinformatics approaches to address the specific research questions. These include identifying differentially methylated regions with programs like MINFI, cellular deconvolution of methylation signal using custom algorithms, estimation of epigenetic aging using DNAage, and application of machine learning to build predictive models (eg. GLMNet).

PhD Scholarship details

Funding: This is an expression of interest only and does not guarantee a scholarship. The standard scholarship provides a living allowance of $27,596 per annum (2019 rate) indexed annually. The living allowance scholarship is for 3.5 years and the tuition fee scholarship is for four years. Scholarships also include up to $1,500 relocation allowance and Overseas Student Health Cover at single rate, for an international candidate.

Supervisor: A/Prof Rodney Lea

Available to: Domestic and International students

PhD

Eligibility Criteria

The applicant will have an aptitude and interest in fields including data science, bioinformatics, computational genomics and statistical genetics. A basic knowledge and skills in using linux operating systems, biostatistical methods and R programming to analyse data sets is desirable. The applicant will also need to meet the minimum eligibility criteria for admission.

Application Procedure

Interested applicants should send an email expressing their interest along with scanned copies of their academic transcripts, CV, a brief statement of their research interests and a proposal that specifically links them to the research project.

Please send the email expressing interest to Rodney.Lea@newcastle.edu.au by 5pm on 01 May 2019.

Applications Close 01 May 2019


Contact A/Prof Rodney Lea
Phone Please contact via email
Email Rodney.Lea@newcastle.edu.au

PhD and Research MastersFind out more