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PSP-omics Project: Transcriptome and investigation of PSP GWAS genes expression and correlation of genomewide sequencing and proteome
UCL Institute of Neurology, Department of Neurodegenerative Disease
Applications are invited for a 3-year PhD studentship in the Department of Neurodegenerative Disease under the supervision of Dr K Mok and Professor John Hardy. The anticipated start date is 1st October, 2018.
Project
This is part of the PSP-omics project headed by Prof Tom Warner, Director of Queen Square Brain Bank and Dr Kin Mok as investigator in the project.
With the unique collection of flash frozen brain tissue of PSP cases at QSSB and access to state of the art technology, we are in unique position to perform the first comprehensive genomic, transcriptomic and proteomic analysis of the underlying pathogenesis of PSP, studying gene to transcript to protein. It will delineate changes in the DNA sequence (whole-genome sequencing), expression of RNA transcripts (RNA-seq) and ultimately levels of protein (proteomics) that the genes encode and relate them to the neurodegenerative disease process.
This project will create the first comprehensive integrated database of ‘omic’ data from a pathologically diagnosed cohort of PSP patients, comprising clinical, genomic, transcriptomic, proteomic and neuropathological data. This data will be a world first and establish a unique data resource for global research into tau mediated neurodegeneration and engender larger scale collaborative studies.
This main focus of this studentship will be the PSP omics analysis. The student shall work on RNA sequencing data from UCL Genomics centre, and liaise with Queen Square Brain Bank to provide replication samples if need. Data will be aligned and quality controlled. This cleaned expression data will be correlate with the Whole Genome Sequencing data we have obtained from the same cohort. This eQTL and sQTL analysis may include realignment and reanalysis in part of Whole genome sequencing data. The student shall also participate in correlation of the coming proteomics data part in this project.
Together with Juan A. Botía, Universidad de Murcia, Spain, we shall further develop downstream analysis on this dataset to shed light on PSP disease mechanism based on coding and non-coding human variation, systems biology approach to detect pathway and potential differential roles of different brain cell types relevant to PSP.
Funding:
This studentship is funded by grants obtained by Dr Kin Mok and Prof John Hardy for three years. This will include UK/EU University tuition fees and an annual stipend of £16,777 increase annually according to UCL policy. The funding will cover necessary travel to Dr Juan A. Botía’s Lab at Universidad de Murcia, Spain.
Entry Requirements:
Applicants must hold a BA/BSc (1st or 2nd class honours or equivalent) or masters’ degree in one of the following disciplines: genetics, neuroscience, biological sciences or bioinformatics degree. The successful applicant will enrol in the PhD program at UCL.
Background on bioinformatics and basic program skills in Bash script, and R is highly preferred.
The following skills are desirable
Other programming skills in Python and Perl and data management e.g MySQL
Exposure to machine learning
Experience in genetic analysis on exomes/genomes
Experience in application of RNA alignment and analysis
Applications of public database for network analysis
Laboratory experience in handling DNA and RNA samples
Informal Enquiries:
The supervisor of the project, Dr Kin Mok (k.mok@ucl.ac.uk) will take informal enquiries.
Application procedures: Application is by CV (2 pages max) and personal statement outlining motivation for applying and suitability for the post (one page) all in the same document. The document should be named LAST NAME_FIRST NAME, and be emailed to: d.blundred@ucl.ac.uk
Please put “PSPomics studentship” in the subject line.
Closing Date: 19th July 2018