Close
Project: Using whole genome sequencing data to explore evolutionary themes across cancers
- Primary supervisor: Dr Nicholas McGranahan
- Secondary supervisor: Professor Charles Swanton
Closing date: Wednesday 2 May 2018
Description
Next-generation sequencing has revolutionised our understanding of cancer – shedding light on novel cancer genes, revealing many of the exogenous and endogenous processes responsible for generating mutations, as well as uncovering the complex evolutionary histories of many tumours. However, despite these advances, there is currently no mechanisms to standardise the complex analyses that are used or efficient mechanisms for data sharing for cancer. There is a need to explore evolutionary themes across cancers to obtain an in-depth understanding of the processes moulding the cancer genome and identify common therapeutic opportunities. The work undertaken for this project will involve creating a standardised bioinformatics pipeline for exploration of cancer sequencing data. The pipeline will seek to infer the somatic catalogue of mutations and copy number events as well as the evolutionary history of tumours, utilizing both multi-region and single sample whole genome sequencing data. Evolutionary themes across three solid tumour types, lung, breast and prostate will then be explored, to identify similarities and differences in the evolutionary trajectories of tumours from diverse cell-types of origin. The student will be expected to develop methods to explore mutational processes in tumours. Currently, methods to explore mutational signatures generally consider solely the trinucleotide context of each mutation, ignoring, for example, their copy number state or replication timing. Incorporating these important factors into mutational signature analysis will refine our understanding of known processes and shed light on novel processes moulding the genome, which may be therapeutically targetable. More detailed information about the research project is available on request from nicholas.mcgranahan.10@ucl.ac.uk.
- Person specification
Essential
• Minimum upper second class Honours Degree in an associated discipline, or an overseas qualification of an equivalent standard.
• Knowledge of mathematics and statistics
• Experience coding in R
• Preliminary knowledge of research techniques.
• Evidence of motivation for and understanding of the proposed area of study.
• Ability to develop understanding of complex problems and apply in-depth knowledge to address them.
• Potential to develop expertise in new areas of the subject.
• Potential for innovation and initiative, and evidence of an ability to work independently.
• Effective communication skills in both written and spoken English.
Desirable
• Relevant laboratory research experience.
• Experience of working with cancer whole exome/whole genome sequencing data
Students will also need to qualify as UK/EU fee payers and meet UCL general admissions criteria.
- Duties and responsibilities
Research
• To apply highly specialist scientific skills and expertise to lead in the delivery of high quality research and the preparation of high-impact research publications.
• To keep abreast of current developments in this research area.
• To report research progress to the supervisory team, the Cancer Institute, and at scientific conferences and meetings.
• To work with other Scientists within the team as necessary.
• To work safely by adhering to all University policies and practices, including preparing and following laboratory risk assessments, and complying with Health and Safety policies, ethical approval processes and Human Tissue Act guidelines.
Analytical and Judgement Skills
• To demonstrate a high-level of technical and analytical skill to resolve highly complex scenarios, requiring analysis, interpretation and expert judgement to find the most appropriate solutions.
• To identify, interpret and integrate information from a wide variety of sources, and critically evaluate the quality and assumptions of these data.
• To show initiative and the ability to make decisions in areas where no previous work has been undertaken.
• To show awareness of your own developmental needs and undertake appropriate training where appropriate.
• To comply with professional codes of conduct.
- Environment
The UCL Cancer Institute is a state-of-the-art institute to consolidate cancer research at UCL and promote links with our partner teaching hospitals, in order to support excellence in basic and translational studies. The Institute draws together talented scientists who are working together to translate research discoveries into developing kinder, more effective therapies for cancer patients. It is a Cancer Research UK and Experimental Cancer Medicine Centre, and contains approximately 580 staff, including 80 PhD and MD (Res) students and 30-40 MSc students. Core facilities within the Institute include: Genomics Facility (gene expression microarrays); Proteomics Facility; Imaging and Cell Sorting (confocal, time-lapsed microscopy, MoFlo FACS); Pathology Suite (laser capture microdissection, tissue arrays); Experimental Imaging (with UCL Institute of Child Health); and Transgenesis.
Eligibility
Please note students will need a minimum of an upper second class Honours Degree in an associated discipline, or an overseas qualification of equivalent standard, qualify as a UK/EU fee payer and meet UCL general admissions criteria. Please see Personal Specification above for full details.
Applications procedure
To apply for this studentship, you must submit only two documents:
1. Your full CV including a short summary (<500 words) detailing how your experience and ability matches the project and the person specification.
2. A single PDF file containing scans of two reference letters, one of which must be academic, and the award certificate and transcripts showing your unit/module marks for all of your degrees, undergraduate and postgraduate.
If any of your documents are not in English you must submit an official English translation with them. These two documents should then be emailed to ci.scholarships@ucl.ac.uk with the studentship code 'McGranahan 01' and your surname in the subject line of the email.
If your referees wish to submit references separately they should email them to ci.scholarships@ucl.ac.uk from a verifiable academic or professional email address. The studentship code above and your surname must be in the email subject line.
Complete applications must be received by Wednesday 2 May 2018, 17:00 (GMT). Incomplete applications will not be forwarded to the Shortlisting Panel.
Queries about the application procedure or recruitment process should be directed to the Cancer Institute Education Team, ci.scholarships@ucl.ac.uk.