Postdoctoral Training Fellow in Evolutionary Cancer Imaging Analysis

Postdoctoral Training Fellow in Evolutionary Cancer Imaging Analysis

The Francis Crick Institute

London, Greater London, United Kingdom

Job title: Postdoctoral Training Fellow in Evolutionary Cancer Imaging

Analysis

Location: The Francis Crick Institute, Midland Road, London

Contract: Fixed-term (4 years), Full time

Salary: Competitive with benefits, subject to skills and experience

Vacancy ID: 9265

 

Short summary

We are seeking a collaborative and self-motivated bioinformatician Postdoctoral Training Fellow to work on cancer evolutionary biology focussed on multiparametric molecular pathology imaging analysis and integration of highly multiplexed tumour microenvironment mass cytometry and next generation sequence data from the TRACERx longitudinal lung cancer program at the Francis Crick Institute. The successful applicants will join the RUBICON study: a rule book and immune atlas for combination therapy funded in a partnership between CRUK and Industry. These studies represent a multidisciplinary, collaborative research effort that seeks to understand how the tumour microenvironment shapes tumour evolution over the treatment course and to identify optimal immune-oncology intervention points in lung cancer.

Project scope

The post-holder will work with the multidisciplinary RUBICON and TRACERx teams under the co-supervision of Dr. Charles Swanton (Francis Crick Institute) and Dr. Chris Russell (Turing Institute) to develop quantitative molecular pathology imaging tools to quantify dynamic changes in cellular populations as tumours evolve over space and time from primary through to metastatic disease. The postdoc will develop new, and optimize existing, algorithms for the analysis and interpretation of high dimensional imaging mass cytometry data, including cell segmentation and quantification and deconvolution of individual cell types within the tumour microenvironment as well as their spatial and social organisation.

A significant part of this post will involve working with the other data scientists in the group to integrate this dataset with existing and future phylogenetic, genomic, transcriptomic and other orthogonal datasets. The work will leverage over 3000 primary and metastatic tumour regions from 600 patients from the TRACERx lung cancer study and lead to the development of state-of-the-art imaging technologies to establish new treatment paradigms to understand the role of the tumour microenvironment on tumour evolution and adaptation.

The post-holder will have a proven track record of publications and academic achievement, be fluent in at least one programming language, and is expected to have experience in the field of imaging analysis (not necessarily related to digital pathology). Prior cancer research is not essential, indeed, applicants from imaging fields outside cancer research are encouraged. It would also be desirable (but not essential) if the applicant had experience in one or more of the following: experience with deep learning/convolutional neural networks, evolutionary biology, ecology, statistics or mathematics. Prior experience with cell segmentation and CyTOF data is particularly desired.

In this project, duties include but are not limited to:

  • To set up image analysis platforms capable of answering research questions associated with cancer evolutionary biology.
  • To develop novel methods of computational evolutionary pathology analysis.
  • To decipher evolutionary mechanisms during lung cancer progression.
  • To work within the informatics team of the TRACERx program.
  • To provide mathematical and statistical support.
  • To employ novel informatics techniques based on evolutionary principles to the analysis of tumour subclonal evolution.
  • Ensure the necessary computational requirements are met to allow for secure data storage and processing of the TRACERx/RUBICON dataset.
  • To understand cancer biology and the relevant literature sufficiently to take own ideas forward as lead author on new projects.
  • To record all experiments in an accurate, timely and clearly presented manner, and use this to prepare data summaries and reports as and when required.
  • To attend, and report research results at regular group and national meetings.
  • To contribute to the dissemination of scientific results by means of writing papers for publication, and presenting orally and in poster form at national and international meetings.
  • As duties and responsibilities change, the job description will be reviewed and amended in consultation with the post-holder
  • The post-holder will carry out any other duties as are within the scope, spirit and purpose of the job as requested by the line manager or Head of Department/ Division.

TRACERx (TRAcking lung Cancer Evolution through therapy/Rx)

TRACERx is a 10-year project started in 2014 with an expected closure date of 2024. It is the first longitudinal cancer genomics study that forms the first national UK consortium focused on deciphering cancer evolution over space and time. The UK scientific partners include the UCL Cancer Institute, CR-UK London Research Institute (and the Francis Crick Institute), CR-UK Manchester Institute and Biomedical research centres at the University of Leicester and Birmingham. The clinical sites include Thoracic Oncology units at UCL Hospitals, the Christie Hospital, Aberdeen, Birmingham, Leicester, Southampton, Glasgow, Sheffield and Cardiff. Funding is generously provided by CR-UK, the Rosetrees Trust, The Novo Nordisk Foundation and the UCL Biomedical Research Centre (£13 million over 9 years).

TRACERx involves multi-region sequence analyses of lung cancers (5000+ exomes and whole genomes in 850 patients) through the disease course from pre-invasive through to primary and metastatic disease, in order to understand cancer evolutionary life histories in this disease. This work is supported by the excellent bioinformatics facilities already available at the Francis Crick Institute and in our Centre together with substantial investment in bioinformatics staff, data storage and computer processing power. Newly discovered driver events are functionally analysed in preclinical models and validated for drug discovery initiatives as part of the Centre’s program.

The TRACERx project is highly successful, as of 2018 more than 400 patients have been fully analysed, 650 patients recruited, with the initial data already resulting in a flow of high-impact publications, including manuscripts in Nature, Cell, Science and New England Journal of Medicine.

RUBICON (a Rule Book and Immune atlas for COmbinatioN therapy)

Rubicon is a Bristol-Myers Squibb (BMS)-funded study associated with the TRACERx lung cancer clinical program. The aim is to use deep learning and artificial intelligence tools to develop new approaches to lung cancer histopathology analysis and to understand how the lung cancer microenvironment constrains the genomic landscape of the evolving disease. This program will analyse through state of the art tissue CyTOF imaging (and other platforms), hundreds of tumour sections taken spatially and longitudinally during the disease course. The study will develop new pathology imaging tools, in order to make the analysis of hundreds of cell types routine in clinical practice for optimal decision making. The study will also define actionable targets on both cancer and immune cells that are stable throughout the disease course which will lead to new combination clinical trials.

About us

The Francis Crick Institute is a biomedical discovery institute dedicated to understanding the fundamental biology underlying health and disease. Its work is helping to understand why disease develops and to translate discoveries into new ways to prevent, diagnose and treat illnesses such as cancer, heart disease, stroke, infections, and neurodegenerative diseases.

An independent organisation, its founding partners are the Medical Research Council (MRC), Cancer Research UK, Wellcome, UCL (University College London), Imperial College London and King’s College London.

The Crick was formed in 2015, and in 2016 it moved into a new state-of-the-art building in central London which brings together 1500 scientists and support staff working collaboratively across disciplines, making it the biggest biomedical research facility under in one building in Europe.

The Francis Crick Institute will be world-class with a strong national role. Its distinctive vision for excellence includes commitments to collaboration; developing emerging talent and exporting it the rest of the UK; public engagement; and helping turn discoveries into treatments as quickly as possible to improve lives and strengthen the economy.

  • If you are interested in applying for this role, please apply via https://goo.gl/c3a4MD
  • The closing date for applications is 23 December 2018 at 23:30.
  • All offers of employment are subject to successful security screening and continuous eligibility to work in the United Kingdom.

Please apply via recruiter’s website.

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