The computational analysis of chromatin structure in human leukaemia and lymphoma

Lead Institute / Faculty: CSU / Medicine

Main Supervisor: Jonathan Strefford

Other members of the supervisory team: Matthew Rose-Zerilli, Reanta Welewska, Helen McCarthy,
Topher Woelk

Duration of the award: October 2017 – September 2012

Full time or part time: Full time

Project description: The human genome is packed into chromatin, an epigenetic structure that has historically been considered to be benign and repressive. However, we now understand that it is in fact vibrant and alive, continually remodelling, a process that determines transcriptional control, chromosomal segregation, replication, recombination and repair. Cancer development is a complex process involving both genetic and epigenetic changes, with the latter including abnormal modifications to chromatin dynamics driving activation or repression of gene transcription and consequent malignant transformation. Whilst the majority of studies into epigenetic deregulation in cancer to date have focused on DNA methylation, recent technological advances now make it possible to map chromatin landscapes in large patient cohorts. Most notably, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) facilitates open chromatin mapping in scarce clinical samples. To establish the feasibility of large-scale chromatin analysis, we recently analysed patients with chronic lymphocytic leukaemia (CLL), the most common form of the disease in Western populations, to provide a basis for dissecting the regulatory heterogeneity of CLL (Rendeiro et al, Nature Communications, 2016, 7:11938).

We are continuing this work, linking chromatin structure to clinical annotations and biological properties in CLL and other lymphomas. In doing so, we hope to unravel the molecular mechanisms driving cancer development. The successful candidate will enter our MRC DTP 4 year Integrated PhD programme, developing powerful computational skills in the area of cancer epigenetics and next generation sequencing, they will work with world-leaders in these areas, providing real insight into the way cancer develops, observations with real-world clinical application.

Please contact: Professor Jonathan Strefford: [Email Address Removed]

Person Specification: See below.
https://jobs.soton.ac.uk/Upload/vacancies/files/16126/03%20Doctoral%20Researcher%20Person%20Specification_UoS_FoM_PhD.docx

We seek a candidate with the following qualities:
• A genuine enthusiasm for the computational/ bioinformatics analysis of human cancer
• A confident independent attitude enabling them to work collaboratively across the bioinformatics interface, between biologists and computational scientists in Southampton and across Europe.
• A computer scientist with a keen interest in biology, or a biologist with a keenness for bioinformatics.
• A good team worker and communicator.
• An organised thinker, able to drive diverse project aspects and manage time efficiently.

The successful candidate is likely to have the following qualifications:
• A 1stor 2:1 degree in computer or biological sciences and/or second degree with a related Masters

Administrative contact and how to apply:
Please complete the University’s online application form, which you can find at
https://studentrecords.soton.ac.uk/BNNRPROD/bzsksrch.P_Login?pos=4361&majr=4361&term=201718
You should enter Jonathan Strefford as your proposed supervisor. To support your application provide an academic CV (including contact details of two referees), official academic transcripts and a personal statement (outlining your suitability for the studentship, what you hope to achieve from the PhD and your research experience to date).

Informal enquiries relating to the project or candidate suitability should be directed to Jonathan Strefford ([Email Address Removed]).

Closing date: 21st July 2017
Interview date: Week starting 24th July 2017